HiCExplorer trial pipeline

Reality check

Conda environment

The notebook must be launched from the hic environment.

Check with the cell magic %conda info where the shell escape (! or %%bash) looks.

Kernel

Before using this notebook, make sure to use the ‘hic’ kernel.

I might change the env into a seperate HiC env for each of the tools, such as HICExplorer, Cooler/cooltools, etc.

As of this version, there is only one environment in the repo, and it contains both Python, R, and CLI tools for use in HI-C data analysis.

Getting started with an overview

In this notebook, we will use HiCExplorer to analysis Hi-C reads from macaque monkeys. We will follow an example from the HiCExplorer documentation.

First, let’s look at the files we have. They are from SRA, and are Hi-C sequencing data from macaque fibroblasts. The data is generated for the Wang2019 paper.

%%bash 

tree ../data/links/macaque_fastq

tree ../../../../data/macaque_raw/downloaded/

du -ha ../../../../data/macaque_raw/downloaded/*.gz

../data/links/macaque_fastq
├── SRR6502335_1.fastq.gz -> ../../../../../../data/macaque_raw/downloaded/SRR6502335_1.fastq.gz
├── SRR6502335_2.fastq.gz -> ../../../../../../data/macaque_raw/downloaded/SRR6502335_2.fastq.gz
├── SRR6502336_1.fastq.gz -> ../../../../../../data/macaque_raw/downloaded/SRR6502336_1.fastq.gz
├── SRR6502336_2.fastq.gz -> ../../../../../../data/macaque_raw/downloaded/SRR6502336_2.fastq.gz
├── SRR6502337_1.fastq.gz -> ../../../../../../data/macaque_raw/downloaded/SRR6502337_1.fastq.gz
├── SRR6502337_2.fastq.gz -> ../../../../../../data/macaque_raw/downloaded/SRR6502337_2.fastq.gz
├── SRR6502338_1.fastq.gz -> ../../../../../../data/macaque_raw/downloaded/SRR6502338_1.fastq.gz
├── SRR6502338_2.fastq.gz -> ../../../../../../data/macaque_raw/downloaded/SRR6502338_2.fastq.gz
├── SRR6502339_1.fastq.gz -> ../../../../../../data/macaque_raw/downloaded/SRR6502339_1.fastq.gz
└── SRR6502339_2.fastq.gz -> ../../../../../../data/macaque_raw/downloaded/SRR6502339_2.fastq.gz

0 directories, 10 files
../../../../data/macaque_raw/downloaded/
├── rheMac10_Mmul10.zip
├── SraRunTable.txt
├── SRR6502335_1.fastq.gz
├── SRR6502335_2.fastq.gz
├── SRR6502336_1.fastq.gz
├── SRR6502336_2.fastq.gz
├── SRR6502337_1.fastq.gz
├── SRR6502337_2.fastq.gz
├── SRR6502338_1.fastq.gz
├── SRR6502338_2.fastq.gz
├── SRR6502339_1.fastq.gz
└── SRR6502339_2.fastq.gz

0 directories, 12 files
20G ../../../../data/macaque_raw/downloaded/SRR6502335_1.fastq.gz
23G ../../../../data/macaque_raw/downloaded/SRR6502335_2.fastq.gz
16G ../../../../data/macaque_raw/downloaded/SRR6502336_1.fastq.gz
17G ../../../../data/macaque_raw/downloaded/SRR6502336_2.fastq.gz
14G ../../../../data/macaque_raw/downloaded/SRR6502337_1.fastq.gz
17G ../../../../data/macaque_raw/downloaded/SRR6502337_2.fastq.gz
14G ../../../../data/macaque_raw/downloaded/SRR6502338_1.fastq.gz
17G ../../../../data/macaque_raw/downloaded/SRR6502338_2.fastq.gz
7.0G    ../../../../data/macaque_raw/downloaded/SRR6502339_1.fastq.gz
7.6G    ../../../../data/macaque_raw/downloaded/SRR6502339_2.fastq.gz

An overview of the sequences

We can see summary statistics for our sequences in the SraRunTable.txt

import pandas as pd

sra_runtable = pd.read_csv("../../../../data/macaque_raw/downloaded/SraRunTable.txt")
sra_runtable[['Run', 'Bases', 'Bytes', 'source_name']]

Table 2.1: The samples chosen for initial data exploration with HiCExplorer. From NCBI SRA Portal.

	Run	Bases	Bytes	source_name
0	SRR6502335	73201141800	31966430779	fibroblast
1	SRR6502336	65119970100	24433383054	fibroblast
2	SRR6502337	52769196300	23015357755	fibroblast
3	SRR6502338	52378949100	22999581685	fibroblast
4	SRR6502339	28885941600	10960123150	fibroblast

Preparation of the .fastq files

The .fastq files were all prepared using this workflow. Briefly, it does three things on the reference genome (Mmul_10/rheMac10):

1. indexing with bwa index
   
2. indexing with samtools faidx
3. indexing of restriction sites of the used restriction enzyme used (hicFindRestSites)

Then, it maps all the .fastq files (each mate individually) back to the reference genome with bwa mem.

Finally, it builds the .h5 Hi-C matrix with hicBuildMatrix, which includes some quality control of the Hi-C library. The results from the quality control can be viewed here.

But also, they are located in the steps/ folder as a log, so let’s read it into view:

HiCExplorer begins

We wil use the HicExplorer commands in the following order:

• hicNormalize
• hicCorrectMatrix
  • diagnostic_plot
  • correct
• hicPlotMatrix

We already used hicFindRestSites and hicBuildMatrix commands from the HicExplorer tool.

Functions that are also moved into hicstuff.py script for import

# First, we will make a function to read the `.log` file into a `pandas` df. 

import pandas as pd
import glob

# All the files can be assigned to a list with glob.glob:
# logs = glob.glob("../results/SRR*/*.log")
# they can be read with a for loop, but it's too messy to show. 

# The .log file is a tab-separated file with 4 tables, so we have to make our own function to read it
# I wrapped it in a class to save all tables from each log in a single variable. 
class HiCQCLog(): 
    def __init__(self, logfile):
        reader = pd.read_csv(logfile, sep="\t", header=None, iterator=True)
        t1 = reader.get_chunk(4).dropna(axis=1)
        t1.columns=t1.iloc[0]
        self.t1 = t1.drop(0).reset_index()

        t2 = reader.get_chunk(6).dropna(axis=1)
        t2.columns=t2.iloc[0]
        self.t2 = t2.drop(4).reset_index()

        t3 = reader.get_chunk(7) .dropna(axis=1)
        t3.columns=t3.iloc[0]
        self.t3 = t3.drop(10).reset_index()

        t4 = reader.get_chunk(7).dropna(axis=1)
        t4.columns=t4.iloc[0]
        self.t4 = t4.drop(17).reset_index()
        
    def view(self):
        display(self.t1, self.t2, self.t3, self.t4)
  

# Make a function to plot .pngs with matplotlib

import os
import glob
import matplotlib.pyplot as plt
from PIL import Image

def plot_pngs_in_grid(image_folder, suffix=".png", ncol=3):
    """
    Plots all PNG images from a specified folder in a grid.
    
    Parameters:
    image_folder (str): Path to the folder containing the PNG files.
    num_cols (int): Number of columns in the grid layout. Default is 3.
    
    Returns:
    None
    """
    # Find all .png files in the folder
    # with a specified suffix (default: .png)
    print(f"Plotting all images in '{os.path.join(image_folder, f'*{suffix}')}'")
    image_files = glob.glob(os.path.join(image_folder, f'*{suffix}'))

    # If no images found, print a message and return
    if not image_files:
        print(f"No PNG files found in {image_folder}.")
        return
    
    # Calculate the number of rows needed
    num_cols = ncol
    num_images = len(image_files)
    num_rows = (num_images + num_cols - 1) // num_cols  # Ceiling division

    # Create a matplotlib figure
    fig, axes = plt.subplots(num_rows, num_cols, figsize=(15, 5 * num_rows))

    # Flatten axes in case the grid is not a perfect rectangle
    axes = axes.flatten()

    # Loop through image files and plot them
    for i, image_file in enumerate(image_files):
        img = Image.open(image_file)  # Open the image file
        axes[i].imshow(img)
        axes[i].axis('off')  # Turn off axis labels
        axes[i].set_title(os.path.basename(image_file))  # Set image title (filename)

    # Hide any remaining empty subplots if the number of images is not a perfect fit for the grid
    for j in range(i + 1, len(axes)):
        axes[j].axis('off')

    # Adjust layout to fit images and titles nicely
    plt.tight_layout()
    plt.show()

glob.glob(os.path.join("../steps/bwa/QC_all_samples/", f'*.png'))

['../steps/bwa/QC_all_samples/read_orientation.png',
 '../steps/bwa/QC_all_samples/distance.png',
 '../steps/bwa/QC_all_samples/pairs_discarded.png',
 '../steps/bwa/QC_all_samples/unmappable_and_non_unique.png',
 '../steps/bwa/QC_all_samples/pairs_sequenced.png']

Results from bwa

SRR35 = HiCQCLog("../results/SRR6502335_QC/QC.log")
SRR35.view()

!hicQC --logfiles $(echo ../results/*_QC/QC.log) --labels "SRR35" "SRR36" "SRR37" "SRR38" "SRR39" --outputFolder ../steps/bwa/QC_all_samples

plot_pngs_in_grid("../steps/bwa/QC_all_samples/", ncol=2)

Plotting all images in '../steps/bwa/QC_all_samples/*.png'

Normalize matrices

%%bash 

hicNormalize -m ../steps/SRR6502335_matrix.h5 --normalize norm_range -o SRR6502335_norm0_1.h5

Create a diagnostic plot

#! hicexplorer
! hicCorrectMatrix diagnostic_plot --help
#! hicCorrectMatrix correct --help

usage: hicCorrectMatrix diagnostic_plot --matrix hic_matrix.h5 -o file.png

options:
  -h, --help            show this help message and exit

Required arguments:
  --matrix MATRIX, -m MATRIX
                        Name of the Hi-C matrix to correct in .h5 format.
                        (default: None)
  --plotName PLOTNAME, -o PLOTNAME
                        File name to save the diagnostic plot. (default: None)

Optional arguments:
  --chromosomes CHROMOSOMES [CHROMOSOMES ...]
                        List of chromosomes to be included in the iterative
                        correction. The order of the given chromosomes will be
                        then kept for the resulting corrected matrix.
                        (default: None)
  --xMax XMAX           Max value for the x-axis in counts per bin. (default:
                        None)
  --perchr              Compute histogram per chromosome. For samples from
                        cells with uneven number of chromosomes and/or
                        translocations it is advisable to check the histograms
                        per chromosome to find the most conservative
                        `filterThreshold`. (default: False)
  --verbose             Print processing status. (default: False)

Let’s make a loop that produce a diagnostic plot for all matrices in the folder:

%%bash 

for FILE in ../steps/*.h5
do
echo $(basename $FILE _matrix.h5)_diag_plot.png
hicCorrectMatrix diagnostic_plot -m $FILE -o ../figures/$(basename $FILE _matrix.h5)_diag_plot.png
done

SRR6502335_diag_plot.png

INFO:hicexplorer.hicCorrectMatrix:Removing 7859 zero value bins
INFO:hicexplorer.hicCorrectMatrix:mad threshold -2.5428248511904763
INFO:hicexplorer.hicCorrectMatrix:Saving diagnostic plot SRR6502335_diag_plot.png

SRR6502336_diag_plot.png

INFO:hicexplorer.hicCorrectMatrix:Removing 7966 zero value bins
INFO:hicexplorer.hicCorrectMatrix:mad threshold -2.406856232876712
INFO:hicexplorer.hicCorrectMatrix:Saving diagnostic plot SRR6502336_diag_plot.png

SRR6502337_diag_plot.png

INFO:hicexplorer.hicCorrectMatrix:Removing 8187 zero value bins
INFO:hicexplorer.hicCorrectMatrix:mad threshold -2.5774256637168143
INFO:hicexplorer.hicCorrectMatrix:Saving diagnostic plot SRR6502337_diag_plot.png

SRR6502338_diag_plot.png

INFO:hicexplorer.hicCorrectMatrix:Removing 8172 zero value bins
INFO:hicexplorer.hicCorrectMatrix:mad threshold -2.689724621848739
INFO:hicexplorer.hicCorrectMatrix:Saving diagnostic plot SRR6502338_diag_plot.png

SRR6502339_diag_plot.png

INFO:hicexplorer.hicCorrectMatrix:Removing 8969 zero value bins
INFO:hicexplorer.hicCorrectMatrix:mad threshold -2.698
INFO:hicexplorer.hicCorrectMatrix:Saving diagnostic plot SRR6502339_diag_plot.png

plot_pngs_in_grid("../figures/bwa", suffix="diag_plot.png")

Plotting all images in '../figures/bwa/*diag_plot.png'

!hicCorrectMatrix diagnostic_plot -m SRR6502335_norm0_1.h5 -o diag_plot_norm.png

INFO:hicexplorer.hicCorrectMatrix:Removing 13359 zero value bins
INFO:hicexplorer.hicCorrectMatrix:mad threshold -2.0545956094919804
INFO:hicexplorer.hicCorrectMatrix:Saving diagnostic plot diag_plot_norm.png

Correct the matrices

And do the correction with the suggested values and ICE. We are going to produce a corrected matrix for both with and without --perchr (per chromosome) option

%%bash 

hicCorrectMatrix correct -m SRR6502335_norm0_1.h5 -o ./SRR6502335_norm0_1_corrected.h5 \
    --correctionMethod ICE \
    --filterThreshold -2 5

INFO:hicexplorer.hicCorrectMatrix:Removing 13359 zero value bins
INFO:hicexplorer.hicCorrectMatrix:matrix contains 21229234 data points. Sparsity 0.000.
INFO:hicexplorer.hicCorrectMatrix:filtering by z-score
INFO:hicexplorer.iterativeCorrection:starting iterative correction
INFO:hicexplorer.iterativeCorrection:pass 5 Estimated time 0:2:29
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 0.909566849589952 
INFO:hicexplorer.iterativeCorrection:pass 10 Estimated time 0:2:27
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 8.186419342166413 
INFO:hicexplorer.iterativeCorrection:pass 15 Estimated time 0:2:24
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 0.8938109193741166 
INFO:hicexplorer.iterativeCorrection:pass 20 Estimated time 0:2:23
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 7.228200439559446 
INFO:hicexplorer.iterativeCorrection:pass 25 Estimated time 0:2:22
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 0.8790910335275449 
INFO:hicexplorer.iterativeCorrection:pass 30 Estimated time 0:2:21
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 6.4417019516824885 
INFO:hicexplorer.iterativeCorrection:pass 35 Estimated time 0:2:19
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 0.8650482568145657 
INFO:hicexplorer.iterativeCorrection:pass 40 Estimated time 0:2:18
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 5.79991880945091 
INFO:hicexplorer.iterativeCorrection:pass 45 Estimated time 0:2:16
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 0.8515610325149747 
INFO:hicexplorer.iterativeCorrection:pass 50 Estimated time 0:2:15
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 5.270362519101916 
INFO:hicexplorer.iterativeCorrection:pass 55 Estimated time 0:2:13
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 0.8385658927762115 
INFO:hicexplorer.iterativeCorrection:pass 60 Estimated time 0:2:12
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 4.827433615502592 
INFO:hicexplorer.iterativeCorrection:pass 65 Estimated time 0:2:10
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 0.8260196439783102 
INFO:hicexplorer.iterativeCorrection:pass 70 Estimated time 0:2:9
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 4.452080477161172 
INFO:hicexplorer.iterativeCorrection:pass 75 Estimated time 0:2:7
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 0.8138884899499492 
INFO:hicexplorer.iterativeCorrection:pass 80 Estimated time 0:2:6
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 4.130200536278638 
INFO:hicexplorer.iterativeCorrection:pass 85 Estimated time 0:2:4
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 0.8021442447614385 
INFO:hicexplorer.iterativeCorrection:pass 90 Estimated time 0:2:3
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 3.8512580422883165 
INFO:hicexplorer.iterativeCorrection:pass 95 Estimated time 0:2:1
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 0.7907626732591944 
INFO:hicexplorer.iterativeCorrection:pass 100 Estimated time 0:2:0
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 3.6072719429655127 
INFO:hicexplorer.iterativeCorrection:pass 105 Estimated time 0:1:58
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 0.7797225650077778 
INFO:hicexplorer.iterativeCorrection:pass 110 Estimated time 0:1:57
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 3.3921051862474654 
INFO:hicexplorer.iterativeCorrection:pass 115 Estimated time 0:1:56
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 0.7690051179967097 
INFO:hicexplorer.iterativeCorrection:pass 120 Estimated time 0:1:54
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 3.200969091836857 
INFO:hicexplorer.iterativeCorrection:pass 125 Estimated time 0:1:52
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 0.7585934895900657 
INFO:hicexplorer.iterativeCorrection:pass 130 Estimated time 0:1:51
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 3.0300755016903764 
INFO:hicexplorer.iterativeCorrection:pass 135 Estimated time 0:1:50
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 0.7484724565014031 
INFO:hicexplorer.iterativeCorrection:pass 140 Estimated time 0:1:48
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 2.876389735422809 
INFO:hicexplorer.iterativeCorrection:pass 145 Estimated time 0:1:46
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 0.7386281528121921 
INFO:hicexplorer.iterativeCorrection:pass 150 Estimated time 0:1:45
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 2.7374526645210087 
INFO:hicexplorer.iterativeCorrection:pass 155 Estimated time 0:1:43
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 0.7290478657442472 
INFO:hicexplorer.iterativeCorrection:pass 160 Estimated time 0:1:42
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 2.61125069105262 
INFO:hicexplorer.iterativeCorrection:pass 165 Estimated time 0:1:40
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 0.7197198745758879 
INFO:hicexplorer.iterativeCorrection:pass 170 Estimated time 0:1:39
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 2.4961193680916445 
INFO:hicexplorer.iterativeCorrection:pass 175 Estimated time 0:1:37
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 0.7106333219153745 
INFO:hicexplorer.iterativeCorrection:pass 180 Estimated time 0:1:36
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 2.3906709792194154 
INFO:hicexplorer.iterativeCorrection:pass 185 Estimated time 0:1:34
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 0.7017781093737747 
INFO:hicexplorer.iterativeCorrection:pass 190 Estimated time 0:1:33
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 2.2937394223838408 
INFO:hicexplorer.iterativeCorrection:pass 195 Estimated time 0:1:31
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 0.6931448117980591 
INFO:hicexplorer.iterativeCorrection:pass 200 Estimated time 0:1:30
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 2.2043377628045153 
INFO:hicexplorer.iterativeCorrection:pass 205 Estimated time 0:1:28
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 0.6847246057914107 
INFO:hicexplorer.iterativeCorrection:pass 210 Estimated time 0:1:27
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 2.1216251819423557 
INFO:hicexplorer.iterativeCorrection:pass 215 Estimated time 0:1:25
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 0.6765092093873197 
INFO:hicexplorer.iterativeCorrection:pass 220 Estimated time 0:1:24
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 2.0448809803593457 
INFO:hicexplorer.iterativeCorrection:pass 225 Estimated time 0:1:22
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 0.668490830563762 
INFO:hicexplorer.iterativeCorrection:pass 230 Estimated time 0:1:21
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 1.9734839366586194 
INFO:hicexplorer.iterativeCorrection:pass 235 Estimated time 0:1:19
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 0.6606621228701033 
INFO:hicexplorer.iterativeCorrection:pass 240 Estimated time 0:1:18
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 1.9068957766214418 
INFO:hicexplorer.iterativeCorrection:pass 245 Estimated time 0:1:16
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 0.6530161468589186 
INFO:hicexplorer.iterativeCorrection:pass 250 Estimated time 0:1:15
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 1.844647827663914 
INFO:hicexplorer.iterativeCorrection:pass 255 Estimated time 0:1:13
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 0.645546336316785 
INFO:hicexplorer.iterativeCorrection:pass 260 Estimated time 0:1:12
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 1.7863301645435703 
INFO:hicexplorer.iterativeCorrection:pass 265 Estimated time 0:1:10
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 0.6382464685075324 
INFO:hicexplorer.iterativeCorrection:pass 270 Estimated time 0:1:9
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 1.7315827201333889 
INFO:hicexplorer.iterativeCorrection:pass 275 Estimated time 0:1:7
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 0.6311106378031317 
INFO:hicexplorer.iterativeCorrection:pass 280 Estimated time 0:1:6
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 1.680087958547833 
INFO:hicexplorer.iterativeCorrection:pass 285 Estimated time 0:1:4
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 0.6241332321985289 
INFO:hicexplorer.iterativeCorrection:pass 290 Estimated time 0:1:3
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 1.6315647996490972 
INFO:hicexplorer.iterativeCorrection:pass 295 Estimated time 0:1:1
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 0.6173089122990445 
INFO:hicexplorer.iterativeCorrection:pass 300 Estimated time 0:0:60
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 1.585763552799874 
INFO:hicexplorer.iterativeCorrection:pass 305 Estimated time 0:0:58
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 0.6106325924406156 
INFO:hicexplorer.iterativeCorrection:pass 310 Estimated time 0:0:57
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 1.542461669855522 
INFO:hicexplorer.iterativeCorrection:pass 315 Estimated time 0:0:55
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 0.604099423659678 
INFO:hicexplorer.iterativeCorrection:pass 320 Estimated time 0:0:54
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 1.501460167201333 
INFO:hicexplorer.iterativeCorrection:pass 325 Estimated time 0:0:52
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 0.5977047782747636 
INFO:hicexplorer.iterativeCorrection:pass 330 Estimated time 0:0:51
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 1.4625805972958585 
INFO:hicexplorer.iterativeCorrection:pass 335 Estimated time 0:0:49
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 0.5914442358786719 
INFO:hicexplorer.iterativeCorrection:pass 340 Estimated time 0:0:48
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 1.4256624739653576 
INFO:hicexplorer.iterativeCorrection:pass 345 Estimated time 0:0:46
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 0.5853135705702154 
INFO:hicexplorer.iterativeCorrection:pass 350 Estimated time 0:0:45
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 1.3905610742802716 
INFO:hicexplorer.iterativeCorrection:pass 355 Estimated time 0:0:43
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 0.5793087392795395 
INFO:hicexplorer.iterativeCorrection:pass 360 Estimated time 0:0:42
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 1.357145554466836 
INFO:hicexplorer.iterativeCorrection:pass 365 Estimated time 0:0:40
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 0.5734258710618427 
INFO:hicexplorer.iterativeCorrection:pass 370 Estimated time 0:0:39
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 1.325297328884087 
INFO:hicexplorer.iterativeCorrection:pass 375 Estimated time 0:0:37
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 0.5676612572517955 
INFO:hicexplorer.iterativeCorrection:pass 380 Estimated time 0:0:36
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 1.2949086703183554 
INFO:hicexplorer.iterativeCorrection:pass 385 Estimated time 0:0:34
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 0.5620113423856818 
INFO:hicexplorer.iterativeCorrection:pass 390 Estimated time 0:0:33
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 1.2658814972347767 
INFO:hicexplorer.iterativeCorrection:pass 395 Estimated time 0:0:31
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 0.5564727158107357 
INFO:hicexplorer.iterativeCorrection:pass 400 Estimated time 0:0:30
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 1.2381263195753522 
INFO:hicexplorer.iterativeCorrection:pass 405 Estimated time 0:0:28
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 0.5510421039116955 
INFO:hicexplorer.iterativeCorrection:pass 410 Estimated time 0:0:27
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 1.2115613195100305 
INFO:hicexplorer.iterativeCorrection:pass 415 Estimated time 0:0:25
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 0.5457163628935884 
INFO:hicexplorer.iterativeCorrection:pass 420 Estimated time 0:0:24
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 1.1861115474657904 
INFO:hicexplorer.iterativeCorrection:pass 425 Estimated time 0:0:22
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 0.5404924720673956 
INFO:hicexplorer.iterativeCorrection:pass 430 Estimated time 0:0:21
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 1.1617082169612458 
INFO:hicexplorer.iterativeCorrection:pass 435 Estimated time 0:0:19
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 0.5353675275918063 
INFO:hicexplorer.iterativeCorrection:pass 440 Estimated time 0:0:18
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 1.138288084403169 
INFO:hicexplorer.iterativeCorrection:pass 445 Estimated time 0:0:16
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 0.5303387366298477 
INFO:hicexplorer.iterativeCorrection:pass 450 Estimated time 0:0:15
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 1.115792902168486 
INFO:hicexplorer.iterativeCorrection:pass 455 Estimated time 0:0:13
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 0.5254034118840032 
INFO:hicexplorer.iterativeCorrection:pass 460 Estimated time 0:0:12
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 1.0941689350888613 
INFO:hicexplorer.iterativeCorrection:pass 465 Estimated time 0:0:10
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 0.5205589664775546 
INFO:hicexplorer.iterativeCorrection:pass 470 Estimated time 0:0:9
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 1.073366531945267 
INFO:hicexplorer.iterativeCorrection:pass 475 Estimated time 0:0:7
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 0.5158029091534628 
INFO:hicexplorer.iterativeCorrection:pass 480 Estimated time 0:0:6
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 1.05333974482263 
INFO:hicexplorer.iterativeCorrection:pass 485 Estimated time 0:0:4
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 0.5111328397651806 
INFO:hicexplorer.iterativeCorrection:pass 490 Estimated time 0:0:3
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 1.0340459902146093 
INFO:hicexplorer.iterativeCorrection:pass 495 Estimated time 0:0:1
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 0.5065464450364833 
INFO:hicexplorer.iterativeCorrection:pass 500 Estimated time 0:0:0
INFO:hicexplorer.iterativeCorrection:max delta - 1 = 1.0154457466418232 

!hicInfo -m SRR6502335_norm0_1_corrected.h5

# Matrix information file. Created with HiCExplorer's hicInfo version 3.7.5
File:   SRR6502335_norm0_1_corrected.h5
Size:   298,615
Bin_length: 10000
Sum of matrix:  12588.40042256422
Chromosomes:length: NC_041754.1: 223616942 bp; NW_021160094.1: 26680 bp; NW_021160095.1: 32580 bp; NW_021160096.1: 33548 bp; NW_021160097.1: 37051 bp; NW_021160098.1: 39993 bp; NW_021160099.1: 40438 bp; NW_021160100.1: 43990 bp; NW_021160101.1: 48895 bp; NW_021160102.1: 50188 bp; NW_021160103.1: 51363 bp; NW_021160104.1: 35879 bp; NW_021160105.1: 54860 bp; NW_021160106.1: 55541 bp; NW_021160107.1: 55582 bp; NW_021160108.1: 59940 bp; NW_021160109.1: 82305 bp; NW_021160110.1: 118135 bp; NW_021160111.1: 133025 bp; NW_021160112.1: 52076 bp; NW_021160113.1: 116334 bp; NW_021160114.1: 65914 bp; NC_041755.1: 196197964 bp; NW_021160115.1: 30586 bp; NW_021160116.1: 35391 bp; NW_021160117.1: 40656 bp; NW_021160118.1: 51074 bp; NW_021160119.1: 48342 bp; NW_021160120.1: 52951 bp; NW_021160121.1: 86201 bp; NW_021160122.1: 92040 bp; NW_021160123.1: 52934 bp; NW_021160124.1: 54780 bp; NC_041756.1: 185288947 bp; NW_021160125.1: 25300 bp; NW_021160126.1: 29349 bp; NW_021160127.1: 29445 bp; NW_021160128.1: 29713 bp; NW_021160129.1: 36488 bp; NW_021160130.1: 29788 bp; NW_021160131.1: 42544 bp; NW_021160132.1: 43837 bp; NW_021160133.1: 51062 bp; NW_021160134.1: 54307 bp; NW_021160135.1: 54760 bp; NW_021160136.1: 59741 bp; NW_021160137.1: 70296 bp; NW_021160138.1: 72641 bp; NW_021160139.1: 94715 bp; NW_021160140.1: 130268 bp; NW_021160141.1: 134158 bp; NW_021160142.1: 47814 bp; NW_021160143.1: 30503 bp; NW_021160144.1: 1229889 bp; NC_041757.1: 169963040 bp; NW_021160145.1: 26875 bp; NW_021160146.1: 27011 bp; NW_021160147.1: 30037 bp; NW_021160148.1: 34319 bp; NW_021160149.1: 36085 bp; NW_021160150.1: 37498 bp; NW_021160151.1: 45706 bp; NW_021160152.1: 47138 bp; NW_021160153.1: 52252 bp; NW_021160154.1: 54371 bp; NW_021160155.1: 54530 bp; NW_021160156.1: 54679 bp; NW_021160157.1: 60005 bp; NW_021160158.1: 75365 bp; NW_021160159.1: 85793 bp; NW_021160160.1: 90302 bp; NW_021160161.1: 738392 bp; NC_041758.1: 187317192 bp; NW_021160162.1: 26685 bp; NW_021160163.1: 29791 bp; NW_021160164.1: 32640 bp; NW_021160165.1: 34222 bp; NW_021160166.1: 35517 bp; NW_021160167.1: 37838 bp; NW_021160168.1: 41651 bp; NW_021160169.1: 41841 bp; NW_021160170.1: 36351 bp; NW_021160171.1: 48938 bp; NW_021160172.1: 56442 bp; NW_021160173.1: 68769 bp; NW_021160174.1: 103593 bp; NW_021160175.1: 185143 bp; NW_021160176.1: 39093 bp; NC_041759.1: 179085566 bp; NW_021160177.1: 27603 bp; NW_021160178.1: 28241 bp; NW_021160179.1: 38876 bp; NW_021160180.1: 39393 bp; NW_021160181.1: 47332 bp; NW_021160182.1: 58084 bp; NW_021160183.1: 57998 bp; NW_021160184.1: 61300 bp; NW_021160185.1: 62126 bp; NW_021160186.1: 64491 bp; NW_021160187.1: 76406 bp; NW_021160188.1: 82950 bp; NW_021160189.1: 101334 bp; NW_021160190.1: 35732 bp; NC_041760.1: 169868564 bp; NW_021160191.1: 27859 bp; NW_021160192.1: 28798 bp; NW_021160193.1: 31162 bp; NW_021160194.1: 35826 bp; NW_021160195.1: 41366 bp; NW_021160196.1: 46105 bp; NW_021160197.1: 51812 bp; NW_021160198.1: 53832 bp; NW_021160199.1: 55920 bp; NW_021160200.1: 58999 bp; NW_021160201.1: 61446 bp; NW_021160202.1: 65479 bp; NW_021160203.1: 72206 bp; NW_021160204.1: 72836 bp; NW_021160205.1: 73247 bp; NW_021160206.1: 83758 bp; NW_021160207.1: 98820 bp; NW_021160208.1: 31768 bp; NC_041761.1: 145679320 bp; NW_021160209.1: 669983 bp; NW_021160210.1: 32194 bp; NW_021160211.1: 133312 bp; NW_021160212.1: 35273 bp; NW_021160213.1: 35782 bp; NW_021160214.1: 36168 bp; NW_021160215.1: 38408 bp; NW_021160216.1: 28604 bp; NW_021160217.1: 45844 bp; NW_021160218.1: 54299 bp; NW_021160219.1: 59871 bp; NW_021160220.1: 66719 bp; NW_021160221.1: 70864 bp; NW_021160222.1: 76376 bp; NW_021160223.1: 83314 bp; NW_021160224.1: 29721 bp; NW_021160225.1: 53832 bp; NC_041762.1: 134124166 bp; NW_021160226.1: 36031 bp; NW_021160227.1: 39733 bp; NW_021160228.1: 47833 bp; NW_021160229.1: 47980 bp; NW_021160230.1: 52082 bp; NW_021160231.1: 54497 bp; NW_021160232.1: 56716 bp; NW_021160233.1: 64642 bp; NW_021160234.1: 65546 bp; NW_021160235.1: 66711 bp; NW_021160236.1: 77799 bp; NW_021160237.1: 85724 bp; NW_021160238.1: 104447 bp; NW_021160239.1: 29162 bp; NW_021160240.1: 47554 bp; NC_041763.1: 99517758 bp; NW_021160241.1: 29490 bp; NW_021160242.1: 29551 bp; NW_021160243.1: 31521 bp; NW_021160244.1: 35220 bp; NW_021160245.1: 43762 bp; NW_021160246.1: 43668 bp; NW_021160247.1: 45264 bp; NW_021160248.1: 74751 bp; NW_021160249.1: 75692 bp; NW_021160250.1: 64301 bp; NW_021160251.1: 84426 bp; NW_021160252.1: 88635 bp; NW_021160253.1: 115549 bp; NW_021160254.1: 31739 bp; NC_041764.1: 133066086 bp; NW_021160255.1: 28076 bp; NW_021160256.1: 30974 bp; NW_021160257.1: 34094 bp; NW_021160258.1: 35836 bp; NW_021160259.1: 36993 bp; NW_021160260.1: 42603 bp; NW_021160261.1: 44793 bp; NW_021160262.1: 36901 bp; NW_021160263.1: 52625 bp; NW_021160264.1: 65186 bp; NW_021160265.1: 70089 bp; NW_021160266.1: 75026 bp; NW_021160267.1: 86584 bp; NW_021160268.1: 67726 bp; NC_041765.1: 130043856 bp; NW_021160269.1: 30461 bp; NW_021160270.1: 34828 bp; NW_021160271.1: 34758 bp; NW_021160272.1: 34993 bp; NW_021160273.1: 40200 bp; NW_021160274.1: 35195 bp; NW_021160275.1: 39160 bp; NC_041766.1: 108737130 bp; NW_021160276.1: 53508 bp; NW_021160277.1: 44853 bp; NW_021160278.1: 55639 bp; NW_021160279.1: 65990 bp; NW_021160280.1: 57542 bp; NW_021160281.1: 89870 bp; NW_021160282.1: 123715 bp; NC_041767.1: 128056306 bp; NW_021160283.1: 32550 bp; NW_021160284.1: 34793 bp; NW_021160285.1: 44605 bp; NW_021160286.1: 36893 bp; NW_021160287.1: 37575 bp; NW_021160288.1: 37831 bp; NW_021160289.1: 37661 bp; NW_021160290.1: 44420 bp; NW_021160291.1: 45281 bp; NW_021160292.1: 46256 bp; NW_021160293.1: 52830 bp; NW_021160294.1: 79630 bp; NW_021160295.1: 82543 bp; NW_021160296.1: 51233 bp; NW_021160297.1: 56227 bp; NW_021160298.1: 27245 bp; NW_021160299.1: 29900 bp; NW_021160300.1: 62273 bp; NC_041768.1: 113283604 bp; NW_021160301.1: 35411 bp; NW_021160302.1: 36170 bp; NW_021160303.1: 38712 bp; NW_021160304.1: 39777 bp; NW_021160305.1: 40306 bp; NW_021160306.1: 39466 bp; NW_021160307.1: 52687 bp; NW_021160308.1: 53925 bp; NW_021160309.1: 53926 bp; NW_021160310.1: 58262 bp; NW_021160311.1: 78748 bp; NW_021160312.1: 88419 bp; NW_021160313.1: 94627 bp; NW_021160314.1: 27791 bp; NC_041769.1: 79627064 bp; NW_021160315.1: 28177 bp; NW_021160316.1: 33884 bp; NW_021160317.1: 34745 bp; NW_021160318.1: 50438 bp; NW_021160319.1: 43437 bp; NW_021160320.1: 52552 bp; NW_021160321.1: 54058 bp; NW_021160322.1: 54071 bp; NW_021160323.1: 54349 bp; NW_021160324.1: 63611 bp; NW_021160325.1: 65150 bp; NW_021160326.1: 65140 bp; NW_021160327.1: 65979 bp; NW_021160328.1: 63325 bp; NW_021160329.1: 53701 bp; NW_021160330.1: 27229 bp; NC_041770.1: 95433459 bp; NW_021160331.1: 25947 bp; NW_021160332.1: 181889 bp; NW_021160333.1: 31091 bp; NW_021160334.1: 31166 bp; NW_021160335.1: 31184 bp; NW_021160336.1: 31250 bp; NW_021160337.1: 43610 bp; NW_021160338.1: 37523 bp; NW_021160339.1: 38541 bp; NW_021160340.1: 45093 bp; NW_021160341.1: 46306 bp; NW_021160342.1: 46347 bp; NW_021160343.1: 50375 bp; NW_021160344.1: 59026 bp; NW_021160345.1: 61686 bp; NW_021160346.1: 61907 bp; NW_021160347.1: 165269 bp; NW_021160348.1: 27125 bp; NW_021160349.1: 15354 bp; NC_041771.1: 74474043 bp; NW_021160350.1: 32300 bp; NW_021160351.1: 37145 bp; NW_021160352.1: 37664 bp; NW_021160353.1: 41176 bp; NW_021160354.1: 41974 bp; NW_021160355.1: 55554 bp; NW_021160356.1: 76316 bp; NC_041772.1: 58315233 bp; NW_021160357.1: 30450 bp; NW_021160358.1: 39455 bp; NW_021160359.1: 41056 bp; NW_021160360.1: 44182 bp; NW_021160361.1: 47076 bp; NW_021160362.1: 53667 bp; NW_021160363.1: 60928 bp; NW_021160364.1: 61817 bp; NW_021160365.1: 66433 bp; NW_021160366.1: 71257 bp; NW_021160367.1: 76390 bp; NW_021160368.1: 78939 bp; NW_021160369.1: 81779 bp; NW_021160370.1: 89493 bp; NW_021160371.1: 90411 bp; NW_021160372.1: 134439 bp; NW_021160373.1: 58152 bp; NW_021160374.1: 124323 bp; NW_021160375.1: 183828 bp; NW_021160376.1: 862827 bp; NC_041773.1: 77137495 bp; NW_021160377.1: 26276 bp; NW_021160378.1: 34752 bp; NW_021160379.1: 36919 bp; NW_021160380.1: 64383 bp; NC_041774.1: 153388924 bp; NW_021160381.1: 48696 bp; NW_021160382.1: 50511 bp; NW_021160383.1: 68997 bp; NW_021160384.1: 79627 bp; NC_027914.1: 11753682 bp; NW_021160385.1: 16018 bp; NW_021160386.1: 16072 bp; NW_021160387.1: 15993 bp; NW_021160388.1: 16197 bp; NW_021160389.1: 16074 bp; NW_021160390.1: 16042 bp; NW_021160391.1: 16077 bp; NW_021160392.1: 15853 bp; NW_021160393.1: 15981 bp; NW_021160394.1: 16244 bp; NW_021160395.1: 32289 bp; NW_021160396.1: 16160 bp; NW_021160397.1: 16187 bp; NW_021160398.1: 16363 bp; NW_021160399.1: 16120 bp; NW_021160400.1: 16055 bp; NW_021160401.1: 16274 bp; NW_021160402.1: 16364 bp; NW_021160403.1: 16225 bp; NW_021160404.1: 16356 bp; NW_021160405.1: 16255 bp; NW_021160406.1: 27321 bp; NW_021160407.1: 16236 bp; NW_021160408.1: 16356 bp; NW_021160409.1: 16461 bp; NW_021160410.1: 16455 bp; NW_021160411.1: 16383 bp; NW_021160412.1: 16352 bp; NW_021160413.1: 15013 bp; NW_021160414.1: 16280 bp; NW_021160415.1: 16551 bp; NW_021160416.1: 16444 bp; NW_021160417.1: 56609 bp; NW_021160418.1: 16439 bp; NW_021160419.1: 16412 bp; NW_021160420.1: 16632 bp; NW_021160421.1: 16299 bp; NW_021160422.1: 16406 bp; NW_021160423.1: 16596 bp; NW_021160424.1: 16436 bp; NW_021160425.1: 16779 bp; NW_021160426.1: 16773 bp; NW_021160427.1: 13224 bp; NW_021160428.1: 14311 bp; NW_021160429.1: 16475 bp; NW_021160430.1: 16734 bp; NW_021160431.1: 15042 bp; NW_021160432.1: 16653 bp; NW_021160433.1: 16729 bp; NW_021160434.1: 16730 bp; NW_021160435.1: 16370 bp; NW_021160436.1: 16749 bp; NW_021160437.1: 16651 bp; NW_021160438.1: 16692 bp; NW_021160439.1: 24869 bp; NW_021160440.1: 16634 bp; NW_021160441.1: 16844 bp; NW_021160442.1: 16892 bp; NW_021160443.1: 16406 bp; NW_021160444.1: 16960 bp; NW_021160445.1: 16925 bp; NW_021160446.1: 16946 bp; NW_021160447.1: 17035 bp; NW_021160448.1: 16874 bp; NW_021160449.1: 16960 bp; NW_021160450.1: 15132 bp; NW_021160451.1: 17048 bp; NW_021160452.1: 16930 bp; NW_021160453.1: 16900 bp; NW_021160454.1: 16782 bp; NW_021160455.1: 16399 bp; NW_021160456.1: 17005 bp; NW_021160457.1: 16760 bp; NW_021160458.1: 16880 bp; NW_021160459.1: 16975 bp; NW_021160460.1: 13066 bp; NW_021160461.1: 17407 bp; NW_021160462.1: 17041 bp; NW_021160463.1: 17431 bp; NW_021160464.1: 17069 bp; NW_021160465.1: 17372 bp; NW_021160466.1: 25112 bp; NW_021160467.1: 16450 bp; NW_021160468.1: 16857 bp; NW_021160469.1: 17184 bp; NW_021160470.1: 17258 bp; NW_021160471.1: 17214 bp; NW_021160472.1: 14066 bp; NW_021160473.1: 17331 bp; NW_021160474.1: 17274 bp; NW_021160475.1: 17243 bp; NW_021160476.1: 17185 bp; NW_021160477.1: 16695 bp; NW_021160478.1: 17197 bp; NW_021160479.1: 17342 bp; NW_021160480.1: 17231 bp; NW_021160481.1: 17498 bp; NW_021160482.1: 17275 bp; NW_021160483.1: 29983 bp; NW_021160484.1: 17398 bp; NW_021160485.1: 17418 bp; NW_021160486.1: 17582 bp; NW_021160487.1: 17409 bp; NW_021160488.1: 17349 bp; NW_021160489.1: 17478 bp; NW_021160490.1: 17439 bp; NW_021160491.1: 17634 bp; NW_021160492.1: 17843 bp; NW_021160493.1: 17802 bp; NW_021160494.1: 31063 bp; NW_021160495.1: 823856 bp; NW_021160496.1: 17707 bp; NW_021160497.1: 9903 bp; NW_021160498.1: 17583 bp; NW_021160499.1: 17715 bp; NW_021160500.1: 17761 bp; NW_021160501.1: 17739 bp; NW_021160502.1: 17822 bp; NW_021160503.1: 17886 bp; NW_021160504.1: 17447 bp; NW_021160505.1: 17932 bp; NW_021160506.1: 37152 bp; NW_021160507.1: 17654 bp; NW_021160508.1: 17964 bp; NW_021160509.1: 17871 bp; NW_021160510.1: 17895 bp; NW_021160511.1: 18023 bp; NW_021160512.1: 17833 bp; NW_021160513.1: 17917 bp; NW_021160514.1: 18018 bp; NW_021160515.1: 17912 bp; NW_021160516.1: 17825 bp; NW_021160517.1: 45053 bp; NW_021160518.1: 17844 bp; NW_021160519.1: 25372 bp; NW_021160520.1: 17956 bp; NW_021160521.1: 18075 bp; NW_021160522.1: 17870 bp; NW_021160523.1: 18079 bp; NW_021160524.1: 18166 bp; NW_021160525.1: 18142 bp; NW_021160526.1: 18128 bp; NW_021160527.1: 18335 bp; NW_021160528.1: 30841 bp; NW_021160529.1: 18029 bp; NW_021160530.1: 18339 bp; NW_021160531.1: 18298 bp; NW_021160532.1: 17970 bp; NW_021160533.1: 4886 bp; NW_021160534.1: 17870 bp; NW_021160535.1: 18327 bp; NW_021160536.1: 18353 bp; NW_021160537.1: 18435 bp; NW_021160538.1: 18512 bp; 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NW_021162611.1: 9085 bp; NW_021162612.1: 9612 bp; NW_021162613.1: 9516 bp; NW_021162614.1: 9842 bp; NW_021162615.1: 9640 bp; NW_021162616.1: 9518 bp; NW_021162617.1: 9669 bp; NW_021162618.1: 8874 bp; NW_021162619.1: 9671 bp; NW_021162620.1: 9721 bp; NW_021162621.1: 9770 bp; NW_021162622.1: 9801 bp; NW_021162623.1: 9694 bp; NW_021162624.1: 9745 bp; NW_021162625.1: 8920 bp; NW_021162626.1: 9820 bp; NW_021162627.1: 9806 bp; NW_021162628.1: 4263 bp; NW_021162629.1: 8779 bp; NW_021162630.1: 9863 bp; NW_021162631.1: 9807 bp; NW_021162632.1: 8623 bp; NW_021162633.1: 9868 bp; NW_021162634.1: 9151 bp; NW_021162635.1: 9955 bp; NW_021162636.1: 9924 bp; NW_021162637.1: 9838 bp; NW_021162638.1: 10004 bp; NW_021162639.1: 9955 bp; NW_021162640.1: 10003 bp; NW_021162641.1: 9999 bp; NW_021162642.1: 9921 bp; NW_021162643.1: 25415 bp; NW_021162644.1: 9991 bp; NW_021162645.1: 9924 bp; NW_021162646.1: 10073 bp; NW_021162647.1: 10228 bp; NW_021162648.1: 10058 bp; NW_021162649.1: 9940 bp; NW_021162650.1: 10204 bp; NW_021162651.1: 10111 bp; NW_021162652.1: 10182 bp; NW_021162653.1: 10313 bp; NW_021162654.1: 11492 bp; NW_021162655.1: 10100 bp; NW_021162656.1: 10334 bp; NW_021162657.1: 9439 bp; NW_021162658.1: 10406 bp; NW_021162659.1: 10221 bp; NW_021162660.1: 10498 bp; NW_021162661.1: 10400 bp; NW_021162662.1: 10024 bp; NW_021162663.1: 10268 bp; NW_021162664.1: 10381 bp; NW_021162665.1: 3153 bp; NW_021162666.1: 10367 bp; NW_021162667.1: 10346 bp; NW_021162668.1: 10300 bp; NW_021162669.1: 10178 bp; NW_021162670.1: 10400 bp; NW_021162671.1: 10505 bp; NW_021162672.1: 10468 bp; NW_021162673.1: 10600 bp; NW_021162674.1: 10579 bp; NW_021162675.1: 10646 bp; NW_021162676.1: 10686 bp; NW_021162677.1: 10682 bp; NW_021162678.1: 10737 bp; NW_021162679.1: 10629 bp; NW_021162680.1: 10838 bp; NW_021162681.1: 10719 bp; NW_021162682.1: 10694 bp; NW_021162683.1: 10866 bp; NW_021162684.1: 10710 bp; NW_021162685.1: 10782 bp; NW_021162686.1: 10247 bp; NW_021162687.1: 10847 bp; NW_021162688.1: 10707 bp; NW_021162689.1: 10888 bp; NW_021162690.1: 10899 bp; NW_021162691.1: 10903 bp; NW_021162692.1: 10977 bp; NW_021162693.1: 10943 bp; NW_021162694.1: 10982 bp; NW_021162695.1: 10633 bp; NW_021162696.1: 11007 bp; NW_021162697.1: 10304 bp; NW_021162698.1: 11099 bp; NW_021162699.1: 11107 bp; NW_021162700.1: 11039 bp; NW_021162701.1: 11251 bp; NW_021162702.1: 11004 bp; NW_021162703.1: 11059 bp; NW_021162704.1: 11138 bp; NW_021162705.1: 11275 bp; NW_021162706.1: 18798 bp; NW_021162707.1: 11251 bp; NW_021162708.1: 11159 bp; NW_021162709.1: 11295 bp; NW_021162710.1: 10713 bp; NW_021162711.1: 11243 bp; NW_021162712.1: 11336 bp; NW_021162713.1: 11295 bp; NW_021162714.1: 10843 bp; NW_021162715.1: 11444 bp; NW_021162716.1: 11408 bp; NW_021162717.1: 11390 bp; NW_021162718.1: 11451 bp; NW_021162719.1: 11342 bp; NW_021162720.1: 11412 bp; NW_021162721.1: 11436 bp; NW_021162722.1: 11385 bp; NW_021162723.1: 11568 bp; NW_021162724.1: 11543 bp; NW_021162725.1: 11379 bp; NW_021162726.1: 11498 bp; NW_021162727.1: 11708 bp; NW_021162728.1: 11336 bp; NW_021162729.1: 11621 bp; NW_021162730.1: 11709 bp; NW_021162731.1: 10966 bp; NW_021162732.1: 11620 bp; NW_021162733.1: 11669 bp; NW_021162734.1: 11610 bp; NW_021162735.1: 11454 bp; NW_021162736.1: 11653 bp; NW_021162737.1: 11716 bp; NW_021162738.1: 11745 bp; NW_021162739.1: 11272 bp; NW_021162740.1: 11688 bp; NW_021162741.1: 11680 bp; NW_021162742.1: 11212 bp; NW_021162743.1: 11720 bp; NW_021162744.1: 11426 bp; NW_021162745.1: 11081 bp; NW_021162746.1: 11763 bp; NW_021162747.1: 16742 bp; NW_021162748.1: 11772 bp; NW_021162749.1: 11950 bp; NW_021162750.1: 11503 bp; NW_021162751.1: 11680 bp; NW_021162752.1: 11848 bp; NW_021162753.1: 11928 bp; NW_021162754.1: 12083 bp; NW_021162755.1: 11991 bp; NW_021162756.1: 12067 bp; NW_021162757.1: 11874 bp; NW_021162758.1: 53119 bp; NW_021162759.1: 12136 bp; NW_021162760.1: 12131 bp; NW_021162761.1: 12066 bp; NW_021162762.1: 12222 bp; NW_021162763.1: 12318 bp; NW_021162764.1: 12183 bp; NW_021162765.1: 12257 bp; NW_021162766.1: 12260 bp; NW_021162767.1: 12309 bp; NW_021162768.1: 11586 bp; NW_021162769.1: 35003 bp; NW_021162770.1: 12334 bp; NW_021162771.1: 12248 bp; NW_021162772.1: 12310 bp; NW_021162773.1: 12294 bp; NW_021162774.1: 12204 bp; NW_021162775.1: 12206 bp; NW_021162776.1: 12314 bp; NW_021162777.1: 12386 bp; NW_021162778.1: 12344 bp; NW_021162779.1: 12101 bp; NW_021162780.1: 22552 bp; NW_021162781.1: 12382 bp; NW_021162782.1: 11940 bp; NW_021162783.1: 12042 bp; NW_021162784.1: 12187 bp; NW_021162785.1: 12533 bp; NW_021162786.1: 12614 bp; NW_021162787.1: 12558 bp; NW_021162788.1: 12524 bp; NW_021162789.1: 12451 bp; NW_021162790.1: 12577 bp; NW_021162791.1: 16440 bp; NW_021162792.1: 12603 bp; NW_021162793.1: 10722 bp; NW_021162794.1: 12730 bp; NW_021162795.1: 12735 bp; NW_021162796.1: 12617 bp; NW_021162797.1: 12605 bp; NW_021162798.1: 12700 bp; NW_021162799.1: 12656 bp; NW_021162800.1: 12782 bp; NW_021162801.1: 12738 bp; NW_021162802.1: 22949 bp; NW_021162803.1: 12656 bp; NW_021162804.1: 12593 bp; NW_021162805.1: 12864 bp; NW_021162806.1: 13007 bp; NW_021162807.1: 12702 bp; NW_021162808.1: 12589 bp; NW_021162809.1: 12649 bp; NW_021162810.1: 12804 bp; NW_021162811.1: 12690 bp; NW_021162812.1: 12815 bp; NW_021162813.1: 28396 bp; NW_021162814.1: 12398 bp; NW_021162815.1: 12743 bp; NW_021162816.1: 12714 bp; NW_021162817.1: 12730 bp; NW_021162818.1: 12883 bp; NW_021162819.1: 12752 bp; NW_021162820.1: 12459 bp; NW_021162821.1: 12714 bp; NW_021162822.1: 12857 bp; NW_021162823.1: 12934 bp; NW_021162824.1: 30612 bp; NW_021162825.1: 12987 bp; NW_021162826.1: 12519 bp; NW_021162827.1: 13025 bp; NW_021162828.1: 13122 bp; NW_021162829.1: 13000 bp; NW_021162830.1: 13136 bp; NW_021162831.1: 13048 bp; NW_021162832.1: 13128 bp; NW_021162833.1: 12996 bp; NW_021162834.1: 13132 bp; NW_021162835.1: 38403 bp; NW_021162836.1: 13199 bp; NW_021162837.1: 13158 bp; NW_021162838.1: 13172 bp; NW_021162839.1: 13291 bp; NW_021162840.1: 13314 bp; NW_021162841.1: 13236 bp; NW_021162842.1: 13272 bp; NW_021162843.1: 13331 bp; NW_021162844.1: 13318 bp; NW_021162845.1: 13362 bp; NW_021162846.1: 11310 bp; NW_021162847.1: 13438 bp; NW_021162848.1: 13399 bp; NW_021162849.1: 13338 bp; NW_021162850.1: 13254 bp; NW_021162851.1: 13051 bp; NW_021162852.1: 13388 bp; NW_021162853.1: 13470 bp; NW_021162854.1: 13489 bp; NW_021162855.1: 13617 bp; NW_021162856.1: 13537 bp; NW_021162857.1: 21541 bp; NW_021162858.1: 13465 bp; NW_021162859.1: 13580 bp; NW_021162860.1: 13567 bp; NW_021162861.1: 13681 bp; NW_021162862.1: 13579 bp; NW_021162863.1: 13572 bp; NW_021162864.1: 13688 bp; NW_021162865.1: 13552 bp; NW_021162866.1: 13585 bp; NW_021162867.1: 13614 bp; NW_021162868.1: 14947 bp; NW_021162869.1: 13577 bp; NW_021162870.1: 13370 bp; NW_021162871.1: 13883 bp; NW_021162872.1: 13774 bp; NW_021162873.1: 13859 bp; NW_021162874.1: 13872 bp; NW_021162875.1: 13134 bp; NW_021162876.1: 13732 bp; NW_021162877.1: 13929 bp; NW_021162878.1: 13801 bp; NW_021162879.1: 22858 bp; NW_021162880.1: 13902 bp; NW_021162881.1: 13861 bp; NW_021162882.1: 13953 bp; NW_021162883.1: 13998 bp; NW_021162884.1: 13888 bp; NW_021162885.1: 13803 bp; NW_021162886.1: 14014 bp; NW_021162887.1: 13991 bp; NW_021162888.1: 14204 bp; NW_021162889.1: 14295 bp; NW_021162890.1: 44378 bp; NW_021162891.1: 14056 bp; NW_021162892.1: 13917 bp; NW_021162893.1: 13939 bp; NW_021162894.1: 14104 bp; NW_021162895.1: 13238 bp; NW_021162896.1: 14209 bp; NW_021162897.1: 14220 bp; NW_021162898.1: 14211 bp; NW_021162899.1: 14304 bp; NW_021162900.1: 13549 bp; NW_021162901.1: 32155 bp; NW_021162902.1: 14220 bp; NW_021162903.1: 14158 bp; NW_021162904.1: 14272 bp; NW_021162905.1: 14321 bp; NW_021162906.1: 14317 bp; NW_021162907.1: 14433 bp; NW_021162908.1: 13953 bp; NW_021162909.1: 14498 bp; NW_021162910.1: 14325 bp; NW_021162911.1: 14328 bp; NW_021162912.1: 55060 bp; NW_021162913.1: 14389 bp; NW_021162914.1: 14413 bp; NW_021162915.1: 14460 bp; NW_021162916.1: 14549 bp; NW_021162917.1: 14368 bp; NW_021162918.1: 14509 bp; NW_021162919.1: 14702 bp; NW_021162920.1: 14508 bp; NW_021162921.1: 14393 bp; NW_021162922.1: 14602 bp; NW_021162923.1: 13704 bp; NW_021162924.1: 14195 bp; NW_021162925.1: 14594 bp; NW_021162926.1: 14544 bp; NW_021162927.1: 14591 bp; NW_021162928.1: 14671 bp; NW_021162929.1: 14570 bp; NW_021162930.1: 14577 bp; NW_021162931.1: 14690 bp; NW_021162932.1: 14648 bp; NW_021162933.1: 14727 bp; NW_021162934.1: 25116 bp; NW_021162935.1: 14639 bp; NW_021162936.1: 13671 bp; NW_021162937.1: 14564 bp; NW_021162938.1: 14580 bp; NW_021162939.1: 14794 bp; NW_021162940.1: 14810 bp; NW_021162941.1: 14798 bp; NW_021162942.1: 14675 bp; NW_021162943.1: 14848 bp; NW_021162944.1: 14717 bp; NW_021162945.1: 10281 bp; NW_021162946.1: 14243 bp; NW_021162947.1: 15014 bp; NW_021162948.1: 14871 bp; NW_021162949.1: 14993 bp; NW_021162950.1: 14950 bp; NW_021162951.1: 14818 bp; NW_021162952.1: 14866 bp; NW_021162953.1: 14986 bp; NW_021162954.1: 14931 bp; NW_021162955.1: 14882 bp; NW_021162956.1: 14945 bp; NW_021162957.1: 15028 bp; NW_021162958.1: 15180 bp; NW_021162959.1: 15060 bp; NW_021162960.1: 15321 bp; NW_021162961.1: 14722 bp; NW_021162962.1: 14720 bp; NW_021162963.1: 15258 bp; NW_021162964.1: 15563 bp; NW_021162965.1: 15316 bp; NW_021162966.1: 37796 bp; NW_021162967.1: 15318 bp; NW_021162968.1: 15330 bp; NW_021162969.1: 15517 bp; NW_021162970.1: 15589 bp; NW_021162971.1: 15588 bp; NW_021162972.1: 15338 bp; NW_021162973.1: 15529 bp; NW_021162974.1: 15700 bp; NW_021162975.1: 15590 bp; NW_021162976.1: 8909 bp; NW_021162977.1: 15493 bp; NW_021162978.1: 15549 bp; NW_021162979.1: 14868 bp; NW_021162980.1: 37717 bp; NW_021162981.1: 15306 bp; NW_021162982.1: 15859 bp; NW_021162983.1: 15679 bp; NW_021162984.1: 15846 bp; NW_021162985.1: 15570 bp; NW_021162986.1: 15710 bp; NW_021162987.1: 27507 bp; NW_021162988.1: 15776 bp; NW_021162989.1: 15726 bp; NW_021162990.1: 15964 bp; NW_021162991.1: 15790 bp; NW_021162992.1: 15927 bp; NW_021162993.1: 15944 bp; NW_021162994.1: 15879 bp; NW_021162995.1: 15880 bp; NW_021162996.1: 16121 bp; NW_021162997.1: 16080 bp; NW_021162998.1: 33825 bp; NW_021162999.1: 15822 bp; NW_021163000.1: 16025 bp; NW_021163001.1: 15997 bp; NW_021163002.1: 15858 bp; NW_021163003.1: 16094 bp; NW_021163004.1: 15959 bp; NW_021163005.1: 15799 bp; NW_021163006.1: 15823 bp; NW_021163007.1: 15985 bp; NW_021163008.1: 15913 bp; NW_021163009.1: 26049 bp; NC_005943.1: 16564 bp; 
Non-zero elements:  21,140,807
Minimum (non zero): 3.59173195802721e-05
Maximum:    0.06933028755391794
NaN bins:   20943

!hicMergeMatrixBins -m ../steps/SRR6502335_matrix.h5 -o SRR6502335_nb100 --numBins 100

# Plot chr1 (NC_041755.1)

!hicPlotMatrix -m SRR6502335_norm0_1_corrected.h5 -o SRR6502335_normcorrect_1.png --region NC_041755.1:0-105000000 --dpi 300

INFO:hicexplorer.hicPlotMatrix:Cooler or no cooler: False
INFO:hicexplorer.hicPlotMatrix:min: 3.59173195802721e-05, max: 0.06933028755391794

!hicPlotMatrix -m SRR6502335_norm0_1_corrected.h5 -o SRR6502335_normcorrect_x.png --region NC_041774.1:0-105000000 --log1p --dpi 300

INFO:hicexplorer.hicPlotMatrix:Cooler or no cooler: False
INFO:hicexplorer.hicPlotMatrix:min: 3.59173195802721e-05, max: 0.06933028755391794

Results from bowtie2 --end-to-end

Let’s look at the summary logs for each of the samples

from hicstuff import HiCQCLog, plot_pngs_in_grid

SRR39 = HiCQCLog("../steps/bowtie2/end-to-end/SRR6502339_QC/QC.log")

import os
import pandas as pd
from IPython.display import display, HTML

# Define the base directory
base_dir = "../steps/bowtie2/end-to-end/"

# List of sample directories (subfolders named SRR6502335_QC, SRR6502336_QC, ...)
sample_dirs = [f"SRR65023{n}_QC" for n in range(35, 40)]


# List of images to compare
image_filenames = [
    "distance.png",
    "pairs_discarded.png",
    "pairs_sequenced.png",
    "read_orientation.png",
    "unmappable_and_non_unique.png"
]

# Create an empty dictionary to hold the image paths for each sample
data = {sample: [] for sample in sample_dirs}

# Iterate over each sample folder and populate the paths for each image type
for sample_dir in sample_dirs:
    sample_path = os.path.join(base_dir, sample_dir)
    for image_filename in image_filenames:
        image_path = os.path.join(sample_path, image_filename)
        if os.path.exists(image_path):
            # Use HTML to display the image in a cell
            img_tag = f'<img src="{image_path}" width="400"/>'
            data[sample_dir].append(img_tag)
        else:
            data[sample_dir].append('Image not found')

# Create a DataFrame from the collected data
df = pd.DataFrame(data, index=image_filenames)

# Display the DataFrame as HTML in Jupyter notebook with images
display(HTML(df.to_html(escape=False)))

	SRR6502335_QC	SRR6502336_QC	SRR6502337_QC	SRR6502338_QC	SRR6502339_QC
distance.png
pairs_discarded.png
pairs_sequenced.png
read_orientation.png
unmappable_and_non_unique.png

%%bash

# Use hicQC to compare:

(echo ../steps/bowtie2/end-to-end/*_QC/QC.log)

hicQC --logfiles $(echo ../steps/bowtie2/end-to-end/*_QC/QC.log) --labels "SRR35" "SRR36" "SRR37" "SRR38" "SRR39" --outputFolder ../steps/bowtie2/end-to-end/QC_all_samples

../steps/bowtie2/end-to-end/SRR6502335_QC/QC.log ../steps/bowtie2/end-to-end/SRR6502336_QC/QC.log ../steps/bowtie2/end-to-end/SRR6502337_QC/QC.log ../steps/bowtie2/end-to-end/SRR6502338_QC/QC.log ../steps/bowtie2/end-to-end/SRR6502339_QC/QC.log

plot_pngs_in_grid("../steps/bowtie2/end-to-end/QC_all_samples/", ncol=3)

Results from bowtie2 --local

%%bash

# Use hicQC to compare:

(echo ../steps/bowtie2/*_QC/QC.log)

hicQC --logfiles $(echo ../steps/bowtie2/local/*_QC/QC.log) --labels "SRR35" "SRR36" "SRR37" "SRR38" "SRR39" --outputFolder ../steps/bowtie2/local/QC_all_samples

../steps/bowtie2/*_QC/QC.log

plot_pngs_in_grid("../steps/bowtie2/local/QC_all_samples/")

Comparing QC results from all 3 mappings

Figure 3.1: Comparison of HiCExplorer QC plots for all samples using different alignment tools. The rows represent different QC plots (pairs sequenced, pairs discarded, unmappable/non-unique, distance, and read orientation), and the columns represent the 3 alignments used (BWA, Bowtie2 end-to-end, Bowtie2 local). Generated by hicQC.

Filter the unplaced scaffolds from the mapping

!zcat "../data/links/ucsc_ref/rheMac10.fa.gz" | grep ">" | sed 's/>//' > all_chromosomes.txt

!grep -v "_" all_chromosomes.txt | sort -V > standard_chromosomes.txt

!cat standard_chromosomes.txt | tr '\n' ' ' > chromosome_order.txt

%%bash 

hicAdjustMatrix -m ../steps/bowtie2/local/SRR6502335.cool \
--outFileName filtered_SRR6502335.cool \
--chromosomes $(cat standard_chromosomes.txt | tr '\n' ' ')

# Check the reduction in size

!du -ha ../steps/bowtie2/local/*35.cool -d1

76M ../steps/bowtie2/local/filtered_SRR6502335.cool
80M ../steps/bowtie2/local/SRR6502335.cool

Try to plot the new filtered matrix

First, check the info on the cooler

!hicInfo -m ../steps/bowtie2/local/filtered_SRR6502335.cool

# Matrix information file. Created with HiCExplorer's hicInfo version 3.7.5
File:   ../steps/bowtie2/local/filtered_SRR6502335.cool
Date:   2024-09-24T12:08:51.357930
Genome assembly:    unknown
Size:   285,408
Bin_length: 10000
Chromosomes:length: chr1: 223616942 bp; chr2: 196197964 bp; chr3: 185288947 bp; chr4: 169963040 bp; chr5: 187317192 bp; chr6: 179085566 bp; chr7: 169868564 bp; chr8: 145679320 bp; chr9: 134124166 bp; chr10: 99517758 bp; chr11: 133066086 bp; chr12: 130043856 bp; chr13: 108737130 bp; chr14: 128056306 bp; chr15: 113283604 bp; chr16: 79627064 bp; chr17: 95433459 bp; chr18: 74474043 bp; chr19: 58315233 bp; chr20: 77137495 bp; chrM: 16564 bp; chrX: 153388924 bp; chrY: 11753682 bp; 
Number of chromosomes:  23
Non-zero elements:  36,751,866
The following columns are available: ['chrom' 'start' 'end']


Generated by:   HiCMatrix-17.2
Cooler library version: cooler-0.10.2
HiCMatrix url:  https://github.com/deeptools/HiCMatrix

# Apparently, something went wrong when creating the different binSizes with hicBuildMatrix, so we will create and merge them manually and may convert them into .mcool

!hicMergeMatrixBins --help

usage: hicMergeMatrixBins --matrix matrix.h5 --outFileName OUTFILENAME
                          --numBins int [--runningWindow] [--help] [--version]

Merges bins from a Hi-C matrix. For example, using a matrix containing 5kb
bins, a matrix of 50kb bins can be derived using --numBins 10. From one type
of downstream analysis to another, different bin sizes are used. For example
to call TADs, unmerged matrices are recommended while to display Hi-C
matrices, bins of approximately 2000bp usually yield the best representations
with `hicPlotMatrix` for small regions, and even larger bins (50kb) are
recommended for whole chromosome representations or for `hicPlotDistVsCounts`.

Required arguments:
  --matrix matrix.h5, -m matrix.h5
                        Matrix to reduce in h5 format. (default: None)
  --outFileName OUTFILENAME, -o OUTFILENAME
                        File name to save the resulting matrix. The output is
                        also a .h5 file. But don't add the suffix. (default:
                        None)
  --numBins int, -nb int
                        Number of bins to merge. (default: None)

Optional arguments:
  --runningWindow       Set to merge for using a running window of length
                        --numBins. (default: False)
  --help, -h            Show this help message and exit.
  --version             show program's version number and exit

Merge bins from the raw matrix

!hicMergeMatrixBins -m ../steps/bowtie2/local/matrices/SRR6502335.cool -o ../steps/bowtie2/local/matrices/SRR6502335_50kb.cool -nb 5

WARNING:hicexplorer.hicMergeMatrixBins:*WARNING*: The matrix is probably a corrected matrix that contains NaN bins. This bins can not be merged and are removed. It is preferable to first merge bins in a uncorrected  matrix and then correct the matrix. Correction factors, if present, are removed as well.

!hicMergeMatrixBins -m ../steps/bowtie2/local/matrices/SRR6502335.cool -o ../steps/bowtie2/local/matrices/SRR6502335_100kb.cool -nb 10

WARNING:hicexplorer.hicMergeMatrixBins:*WARNING*: The matrix is probably a corrected matrix that contains NaN bins. This bins can not be merged and are removed. It is preferable to first merge bins in a uncorrected  matrix and then correct the matrix. Correction factors, if present, are removed as well.

Merge bins from the filtered matrix

!hicMergeMatrixBins -m ../steps/bowtie2/local/matrices/filtered_SRR6502335.cool -o ../steps/bowtie2/local/matrices/filtered_SRR6502335_50kb.cool -nb 5

!hicInfo -m ../steps/bowtie2/local/matrices/filtered_SRR6502335_50kb.cool

# Matrix information file. Created with HiCExplorer's hicInfo version 3.7.5
File:   ../steps/bowtie2/local/matrices/filtered_SRR6502335_50kb.cool
Date:   2024-09-24T15:52:47.957236
Genome assembly:    unknown
Size:   56,325
Chromosomes:length: chr1: 223616942 bp; chr2: 196190000 bp; chr3: 185270000 bp; chr4: 169963040 bp; chr5: 187280000 bp; chr6: 179085566 bp; chr7: 169850000 bp; chr8: 145679320 bp; chr9: 134110000 bp; chr10: 99517758 bp; chr11: 133066086 bp; chr12: 130040000 bp; chr13: 108730000 bp; chr14: 128040000 bp; chr15: 113283604 bp; chr16: 79627064 bp; chr17: 95410000 bp; chr18: 74460000 bp; chr19: 58310000 bp; chr20: 77137495 bp; chrX: 153380000 bp; chrY: 11250000 bp; 
Number of chromosomes:  22
Non-zero elements:  24,159,441
The following columns are available: ['chrom' 'start' 'end']


Generated by:   HiCMatrix-17.2
Cooler library version: cooler-0.10.2
HiCMatrix url:  https://github.com/deeptools/HiCMatrix

!hicMergeMatrixBins -m ../steps/bowtie2/local/matrices/filtered_SRR6502335.cool -o ../steps/bowtie2/local/matrices/filtered_SRR6502335_100kb.cool -nb 10

WARNING:hicexplorer.hicMergeMatrixBins:*WARNING*: The matrix is probably a corrected matrix that contains NaN bins. This bins can not be merged and are removed. It is preferable to first merge bins in a uncorrected  matrix and then correct the matrix. Correction factors, if present, are removed as well.

Create plots (each chromosome separately) and compare filtered vs unfiltered matrices

%%bash 

for CHR in $(cat standard_chromosomes.txt)
do 
    echo $CHR
    hicPlotMatrix -m ../steps/bowtie2/local/matrices/SRR6502335_50kb.cool --chromosomeOrder $CHR -o ../figures/bowtie2/local/raw_50kb_$CHR.png --dpi 200
    hicPlotMatrix -m ../steps/bowtie2/local/matrices/filtered_SRR6502335_50kb.cool --chromosomeOrder $CHR -o ../figures/bowtie2/local/raw_filter_50kb_$CHR.png --dpi 200 \
    --increaseFigureWidth 0
    --increaseFigureHeight 0
done

chr1

INFO:hicexplorer.hicPlotMatrix:Cooler or no cooler: True

import os
from natsort import natsorted
import matplotlib.pyplot as plt
from IPython.display import display, Image

# Directory containing the PNG files
directory = '../figures/bowtie2/local/'

# List all raw_chr* files
raw_files = [f for f in os.listdir(directory) if f.startswith('raw_50kb') and f.endswith('.png')]

# List all raw_filter_chr* files
raw_filter_files = [f for f in os.listdir(directory) if f.startswith('raw_filter_50kb') and f.endswith('.png')]

# Sort files using natural sorting
sorted_raw_files = natsorted(raw_files)
sorted_raw_filter_files = natsorted(raw_filter_files)

paired_files = list(zip(sorted_raw_files, sorted_raw_filter_files))

# Plot the images side by side
num_pairs = len(paired_files)
fig, axes = plt.subplots(num_pairs, 2, figsize=(15, 7 * num_pairs))

for i, (raw_file, raw_filter_file) in enumerate(paired_files):
    # Plot raw image
    raw_img_path = os.path.join(directory, raw_file)
    raw_img = plt.imread(raw_img_path)
    axes[i, 0].imshow(raw_img)
    axes[i, 0].axis('off')
    axes[i, 0].set_title(raw_file)

    # Plot raw_filter image
    raw_filter_img_path = os.path.join(directory, raw_filter_file)
    raw_filter_img = plt.imread(raw_filter_img_path)
    axes[i, 1].imshow(raw_filter_img)
    axes[i, 1].axis('off')
    axes[i, 1].set_title(raw_filter_file)

plt.tight_layout()
plt.show()

Pooled samples

Pool the samples (matrices) into one big matrix

%%bash

# Check the sizes of the (unmodified, 10kb binned) matrices
hicInfo -m ../steps/bowtie2/local/matrices/SRR650233{5..9}.cool \
    | grep -E "File|Size" \
    | awk '/File/ {print; next} /Size/ {print $0 "\n"}'

File:   ../steps/bowtie2/local/matrices/SRR6502335.cool
Size:   298,615

File:   ../steps/bowtie2/local/matrices/SRR6502336.cool
Size:   298,615

File:   ../steps/bowtie2/local/matrices/SRR6502337.cool
Size:   298,615

File:   ../steps/bowtie2/local/matrices/SRR6502338.cool
Size:   298,615

File:   ../steps/bowtie2/local/matrices/SRR6502339.cool
Size:   298,615

INFO:hicexplorer.hicPlotMatrix:Cooler or no cooler: True

!hicSumMatrices -m $(echo ../steps/bowtie2/local/matrices/SRR650233{5..9}.cool) -o ../steps/bowtie2/local/matrices/pooled_10kb.cool

%%bash 

hicAdjustMatrix -m ../steps/bowtie2/local/matrices/pooled_10kb.cool \
    --outFileName filtered_pooled_10kb.cool \
    --chromosomes $(cat chromosome_order.txt)

!hicInfo -m ../steps/bowtie2/local/matrices/pooled_10kb.cool | grep -E 'File|Size|Number|Non'
!echo ""
!hicInfo -m ../steps/bowtie2/local/matrices/filtered_pooled_10kb.cool | grep -E 'File|Size|Number|Non'

File:   ../steps/bowtie2/local/matrices/pooled_10kb.cool
Size:   298,615
Number of chromosomes:  2939
Non-zero elements:  117,537,653

File:   ../steps/bowtie2/local/matrices/filtered_pooled_10kb.cool
Size:   285,406
Number of chromosomes:  22
Non-zero elements:  117,090,191

Create different bin sizes (hicMergeMatrixBins)

%%bash 

# This command requires ~14G available memory. 
# hicMergeMatrixBins -m ../steps/bowtie2/local/matrices/filtered_pooled_10kb.cool -o ../steps/bowtie2/local/matrices/filtered_pooled_40kb.cool -nb 4

%%bash 

hicMergeMatrixBins \
    -m ../steps/bowtie2/local/matrices/filtered_pooled_10kb.cool \
    -o ../steps/bowtie2/local/matrices/filtered_pooled_50kb.cool \
    -nb 5 

hicMergeMatrixBins \
    -m ../steps/bowtie2/local/matrices/filtered_pooled_10kb.cool \
    -o ../steps/bowtie2/local/matrices/filtered_pooled_100kb.cool \
    -nb 10

WARNING:hicexplorer.hicMergeMatrixBins:*WARNING*: The matrix is probably a corrected matrix that contains NaN bins. This bins can not be merged and are removed. It is preferable to first merge bins in a uncorrected  matrix and then correct the matrix. Correction factors, if present, are removed as well.
WARNING:hicexplorer.hicMergeMatrixBins:*WARNING*: The matrix is probably a corrected matrix that contains NaN bins. This bins can not be merged and are removed. It is preferable to first merge bins in a uncorrected  matrix and then correct the matrix. Correction factors, if present, are removed as well.

%%bash
hicInfo -m ../steps/bowtie2/local/matrices/filtered_pooled_{10,50,100}kb.cool \
    | grep -E 'File|Size|Number|Non' \
    | sed '/Non/a\\'

File:   ../steps/bowtie2/local/matrices/filtered_pooled_10kb.cool
Size:   285,406
Number of chromosomes:  22
Non-zero elements:  117,090,191

File:   ../steps/bowtie2/local/matrices/filtered_pooled_50kb.cool
Size:   56,129
Number of chromosomes:  22
Non-zero elements:  73,496,938

File:   ../steps/bowtie2/local/matrices/filtered_pooled_100kb.cool
Size:   28,066
Number of chromosomes:  22
Non-zero elements:  55,337,833

Plot the chromosomes (seperately)

%%bash 

#for CHR in $(cat standard_chromosomes.txt)

for CHR in "chrX"

do 
    echo $CHR
    hicPlotMatrix -m ../steps/bowtie2/local/matrices/filtered_pooled_50kb.cool \
    --chromosomeOrder $CHR \
    -o ../figures/bowtie2/local/filter_pooled_50kb_$CHR.png \
    --dpi 200 \
    --colorMap "Reds" \
    --log1p \
    --increaseFigureWidth 0 \
    --increaseFigureHeight 0
done

chrX

INFO:hicexplorer.hicPlotMatrix:Cooler or no cooler: True

from hicstuff import plot_pngs_in_grid as plt

plt("../figures/bowtie2/local/", suffix="filter_pooled_50kb_*", ncol=3)

Diagnostic plot for raw sample

%%bash 

hicCorrectMatrix diagnostic_plot -m ../steps/bowtie2/local/matrices/filtered_pooled_10kb.cool -o ../figures/bowtie2/local/raw/diag_filter_pooled_10kb.png & 
hicCorrectMatrix diagnostic_plot -m ../steps/bowtie2/local/matrices/filtered_pooled_40kb.cool -o ../figures/bowtie2/local/raw/diag_filter_pooled_40kb.png & 
hicCorrectMatrix diagnostic_plot -m ../steps/bowtie2/local/matrices/filtered_pooled_50kb.cool -o ../figures/bowtie2/local/raw/diag_filter_pooled_50kb.png & 
hicCorrectMatrix diagnostic_plot -m ../steps/bowtie2/local/matrices/filtered_pooled_100kb.cool -o ../figures/bowtie2/local/raw/diag_filter_pooled_100kb.png & 

wait

Normalize to the smallest read count (hicNormalize -n smallest -sz 1.0)

!hicNormalize --help

usage: hicNormalize --matrices MATRICES [MATRICES ...] --normalize
                    {norm_range,smallest,multiplicative} --outFileName
                    FILENAME [FILENAME ...]
                    [--multiplicativeValue MULTIPLICATIVEVALUE]
                    [--setToZeroThreshold SETTOZEROTHRESHOLD] [--help]
                    [--version]

Normalizes given matrices either to the smallest given read number of all matrices or to 0 - 1 range. However, it does NOT compute the contact probability.

We recommend to compute first the normalization (with hicNormalize) and correct the data (with hicCorrectMatrix) in a second step.

Required arguments:
  --matrices MATRICES [MATRICES ...], -m MATRICES [MATRICES ...]
                        The matrix (or multiple matrices) to get information
                        about. HiCExplorer supports the following file
                        formats: h5 (native HiCExplorer format) and cool.
  --normalize {norm_range,smallest,multiplicative}, -n {norm_range,smallest,multiplicative}
                        Normalize to a) 0 to 1 range, b) all matrices to the
                        lowest read count of the given matrices (Default:
                        smallest).
  --outFileName FILENAME [FILENAME ...], -o FILENAME [FILENAME ...]
                        Output file name for the Hi-C matrix.

Optional arguments:
  --multiplicativeValue MULTIPLICATIVEVALUE, -mv MULTIPLICATIVEVALUE
                        Value to multiply if --normalize is set to
                        multiplicative. (Default: 1).
  --setToZeroThreshold SETTOZEROTHRESHOLD, -sz SETTOZEROTHRESHOLD
                        A threshold to set all values after normalization to 0
                        if smaller this threshold. Default value is 0 i.e.
                        there is no effect.It is recommended to set it for the
                        normalize mode "smallest" to 1.0. This parameter will
                        influence the sparsity of the matrix by removing many
                        values close to 0 in smallest normalization mode.
  --help, -h            show this help message and exit
  --version             show program's version number and exit

%%bash 

# Try to utilize more than one core (if they have been requested) by submitting lines in the background (with '&')

hicNormalize -m ../steps/bowtie2/local/matrices/filtered_pooled_10kb.cool  -o ../steps/bowtie2/local/matrices/normsm_filtered_pooled_10kb.cool -n smallest -sz 1.0 &
hicNormalize -m ../steps/bowtie2/local/matrices/filtered_pooled_40kb.cool  -o ../steps/bowtie2/local/matrices/normsm_filtered_pooled_40kb.cool -n smallest -sz 1.0 &
hicNormalize -m ../steps/bowtie2/local/matrices/filtered_pooled_50kb.cool  -o ../steps/bowtie2/local/matrices/normsm_filtered_pooled_50kb.cool -n smallest -sz 1.0 &
hicNormalize -m ../steps/bowtie2/local/matrices/filtered_pooled_100kb.cool -o ../steps/bowtie2/local/matrices/normsm_filtered_pooled_100kb.cool -n smallest -sz 1.0 &

wait 

%%bash

hicInfo -m ../steps/bowtie2/local/matrices/normsm_filtered_pooled_{10,40,50,100}kb.cool | grep -E 'File|Size|Number|Non' | sed '/Non/a\\'

File:   ../steps/bowtie2/local/matrices/normsm_filtered_pooled_10kb.cool
Size:   285,406
Number of chromosomes:  22
Non-zero elements:  117,090,191

File:   ../steps/bowtie2/local/matrices/normsm_filtered_pooled_40kb.cool
Size:   70,164
Number of chromosomes:  22
Non-zero elements:  79,495,904

File:   ../steps/bowtie2/local/matrices/normsm_filtered_pooled_50kb.cool
Size:   56,129
Number of chromosomes:  22
Non-zero elements:  73,496,938

File:   ../steps/bowtie2/local/matrices/normsm_filtered_pooled_100kb.cool
Size:   28,066
Number of chromosomes:  22
Non-zero elements:  55,337,833

Plot the normalized, pooled matrix

%%bash

for CHR in $(cat standard_chromosomes.txt)
do 
    echo $CHR
    hicPlotMatrix -m ../steps/bowtie2/local/matrices/normsm_filtered_pooled_40kb.cool --chromosomeOrder $CHR -o ../figures/bowtie2/local/normalized/normsm_filter_pooled_40kb_$CHR.png --dpi 200
    #hicPlotMatrix -m ../steps/bowtie2/local/matrices/normsm_filtered_pooled_50kb.cool --chromosomeOrder $CHR -o ../figures/bowtie2/local/normalized/normsm_filter_pooled_50kb_$CHR.png --dpi 200
done

chr1

INFO:hicexplorer.hicPlotMatrix:Cooler or no cooler: True

chr2

INFO:hicexplorer.hicPlotMatrix:Cooler or no cooler: True

chr3

INFO:hicexplorer.hicPlotMatrix:Cooler or no cooler: True

chr4

INFO:hicexplorer.hicPlotMatrix:Cooler or no cooler: True

chr5

INFO:hicexplorer.hicPlotMatrix:Cooler or no cooler: True

chr6

INFO:hicexplorer.hicPlotMatrix:Cooler or no cooler: True

chr7

INFO:hicexplorer.hicPlotMatrix:Cooler or no cooler: True

chr8

INFO:hicexplorer.hicPlotMatrix:Cooler or no cooler: True

chr9

INFO:hicexplorer.hicPlotMatrix:Cooler or no cooler: True

chr10

INFO:hicexplorer.hicPlotMatrix:Cooler or no cooler: True

chr11

INFO:hicexplorer.hicPlotMatrix:Cooler or no cooler: True

chr12

INFO:hicexplorer.hicPlotMatrix:Cooler or no cooler: True

chr13

INFO:hicexplorer.hicPlotMatrix:Cooler or no cooler: True

chr14

INFO:hicexplorer.hicPlotMatrix:Cooler or no cooler: True

chr15

INFO:hicexplorer.hicPlotMatrix:Cooler or no cooler: True

chr16

INFO:hicexplorer.hicPlotMatrix:Cooler or no cooler: True

chr17

INFO:hicexplorer.hicPlotMatrix:Cooler or no cooler: True

chr18

INFO:hicexplorer.hicPlotMatrix:Cooler or no cooler: True

chr19

INFO:hicexplorer.hicPlotMatrix:Cooler or no cooler: True

chr20

INFO:hicexplorer.hicPlotMatrix:Cooler or no cooler: True

chrX

INFO:hicexplorer.hicPlotMatrix:Cooler or no cooler: True

chrY

INFO:hicexplorer.hicPlotMatrix:Cooler or no cooler: True

Diagnose and correct the normalized, pooled matrix

%%bash 

hicCorrectMatrix diagnostic_plot -m ../steps/bowtie2/local/matrices/normsm_filtered_pooled_10kb.cool -o ../figures/bowtie2/local/normalized/diag_normsm_filter_pooled_10kb.png & 
hicCorrectMatrix diagnostic_plot -m ../steps/bowtie2/local/matrices/normsm_filtered_pooled_40kb.cool  -o ../figures/bowtie2/local/normalized/diag_normsm_filter_pooled_40kb.png & 
hicCorrectMatrix diagnostic_plot -m ../steps/bowtie2/local/matrices/normsm_filtered_pooled_50kb.cool  -o ../figures/bowtie2/local/normalized/diag_normsm_filter_pooled_50kb.png & 
hicCorrectMatrix diagnostic_plot -m ../steps/bowtie2/local/matrices/normsm_filtered_pooled_100kb.cool -o ../figures/bowtie2/local/normalized/diag_normsm_filter_pooled_100kb.png & 

wait

INFO:hicexplorer.hicCorrectMatrix:Removing 0 zero value bins
INFO:hicexplorer.hicCorrectMatrix:mad threshold -3.261957134177215
INFO:hicexplorer.hicCorrectMatrix:Saving diagnostic plot ../figures/bowtie2/local/normalized/diag_normsm_filter_pooled_100kb.png

INFO:hicexplorer.hicCorrectMatrix:Removing 0 zero value bins
INFO:hicexplorer.hicCorrectMatrix:mad threshold -3.3912234086628996
INFO:hicexplorer.hicCorrectMatrix:Saving diagnostic plot ../figures/bowtie2/local/normalized/diag_normsm_filter_pooled_50kb.png

INFO:hicexplorer.hicCorrectMatrix:Removing 0 zero value bins
INFO:hicexplorer.hicCorrectMatrix:mad threshold -3.3260620737327184
INFO:hicexplorer.hicCorrectMatrix:Saving diagnostic plot ../figures/bowtie2/local/normalized/diag_normsm_filter_pooled_40kb.png

INFO:hicexplorer.hicCorrectMatrix:Removing 4762 zero value bins
INFO:hicexplorer.hicCorrectMatrix:mad threshold -2.7562685931558937
INFO:hicexplorer.hicCorrectMatrix:Saving diagnostic plot ../figures/bowtie2/local/normalized/diag_normsm_filter_pooled_10kb.png

from hicstuff import plot_pngs_in_grid as plt
plt("../figures/bowtie2/local/normalized", suffix="diag*", ncol=4)

plt("../figures/bowtie2/local/raw", suffix="diag*", ncol=4)

Plotting all images in '../figures/bowtie2/local/normalized/*diag*':

Plotting all images in '../figures/bowtie2/local/raw/*diag*':

!hicCorrectMatrix correct --help

usage: hicCorrectMatrix correct --matrix hic_matrix.h5 --filterThreshold -1.2 5 (Only if ICE)-out corrected_matrix.h5 

options:
  -h, --help            show this help message and exit

Required arguments:
  --matrix MATRIX, -m MATRIX
                        Name of the Hi-C matrix to correct in .h5 format.
                        (default: None)
  --outFileName OUTFILENAME, -o OUTFILENAME
                        File name to save the resulting matrix. The output is
                        a .h5 file. (default: None)

Optional arguments:
  --correctionMethod STR
                        Method to be used for matrix correction. It can be set
                        to KR or ICE (Default: KR).
  --filterThreshold FILTERTHRESHOLD FILTERTHRESHOLD, -t FILTERTHRESHOLD FILTERTHRESHOLD
                        Removes bins of low or large coverage. Usually these
                        bins do not contain valid Hi-C data or represent
                        regions that accumulate reads and thus must be
                        discarded. Use hicCorrectMatrix diagnostic_plot to
                        identify the modified z-value thresholds. A lower and
                        upper threshold are required separated by space, e.g.
                        --filterThreshold -1.5 5. Applied only for ICE!
                        (default: None)
  --iterNum INT, -n INT
                        Number of iterations to compute.only for ICE!
                        (Default: 500).
  --inflationCutoff INFLATIONCUTOFF
                        Value corresponding to the maximum number of times a
                        bin can be scaled up during the iterative correction.
                        For example, an inflation cutoff of 3 will filter out
                        all bins that were expanded 3 times or more during the
                        iterative correctionself.Only for ICE! (default: None)
  --transCutoff TRANSCUTOFF, -transcut TRANSCUTOFF
                        Clip high counts in the top -transcut trans regions
                        (i.e. between chromosomes). A usual value is 0.05.
                        Only for ICE! (default: None)
  --sequencedCountCutoff SEQUENCEDCOUNTCUTOFF
                        Each bin receives a value indicating the fraction that
                        is covered by reads. A cutoff of 0.5 will discard all
                        those bins that have less than half of the bin
                        covered. Only for ICE! (default: None)
  --chromosomes CHROMOSOMES [CHROMOSOMES ...]
                        List of chromosomes to be included in the iterative
                        correction. The order of the given chromosomes will be
                        then kept for the resulting corrected matrix (default:
                        None)
  --skipDiagonal, -s    If set, diagonal counts are not included. Only for
                        ICE! (default: False)
  --perchr              Normalize each chromosome separately. This is useful
                        for samples from cells with uneven number of
                        chromosomes and/or translocations. (default: False)
  --filteredBed FILTEREDBED
                        Print bins filtered our by --filterThreshold to this
                        file (default: None)
  --verbose             Print processing status. (default: False)
  --version             show program's version number and exit

Correcting the matrices

Is memory-intensive, and was therefore run in a workflow. However, I don’t know if it went well. It spent waay less MEM than documentation suggests.

Plotting the corrected matrices

Chromosome 1

%%bash 

hicPlotMatrix \
    -m ../steps/bowtie2/local/matrices/normsm_filtered_pooled_10kb_corrected.cool \
    -o ../figures/bowtie2/local/normalized/normsm_filter_pooled_10kb_corrected_chr1-20-80Mb.png \
    --region chr1:20000000-80000000 --log1p &

hicPlotMatrix \
    -m ../steps/bowtie2/local/matrices/normsm_filtered_pooled_10kb_corrected.cool \
    -o ../figures/bowtie2/local/normalized/normsm_filter_pooled_10kb_corrected_chr1-50-60Mb.png \
    --region chr1:50000000-60000000 --log1p &

wait

INFO:hicexplorer.hicPlotMatrix:Cooler or no cooler: True
INFO:hicexplorer.hicPlotMatrix:Cooler or no cooler: True

%%bash

hicPlotMatrix \
    -m ../steps/bowtie2/local/matrices/normsm_filtered_pooled_50kb_corrected.cool \
    -o ../figures/bowtie2/local/normalized/normsm_filter_pooled_50kb_corrected_chr1.png \
    --region chr1 --log1p

INFO:hicexplorer.hicPlotMatrix:Cooler or no cooler: True

%%bash

hicPlotMatrix \
    -m ../steps/bowtie2/local/matrices/normsm_filtered_pooled_100kb_corrected.cool \
    -o ../figures/bowtie2/local/normalized/normsm_filter_pooled_100kb_corrected_chr1.png \
    --region chr1 --log1p

INFO:hicexplorer.hicPlotMatrix:Cooler or no cooler: True

from hicstuff import plot_pngs_in_grid as plt

plt("../figures/bowtie2/local/normalized/", suffix="corrected*.png", ncol=2)

Plotting all images in '../figures/bowtie2/local/normalized/*corrected*.png':

Chr12 (as in Wang2019)

%%bash 

hicPlotMatrix \
    -m ../steps/bowtie2/local/matrices/normsm_filtered_pooled_100kb_corrected.cool \
    -o ../figures/bowtie2/local/normalized/normsm_filter_pooled_100kb_corrected_chr12-1-105Mb.png \
    --region chr12:1-105000000 --log1p \
    --colorMap "Reds" &

hicPlotMatrix \
    -m ../steps/bowtie2/local/matrices/normsm_filtered_pooled_50kb_corrected.cool \
    -o ../figures/bowtie2/local/normalized/normsm_filter_pooled_50kb_corrected_chr12-60-70Mb.png \
    --region chr12:60000000-70000000 --log1p \
    --colorMap "Reds" &

hicPlotMatrix \
    -m ../steps/bowtie2/local/matrices/normsm_filtered_pooled_40kb_corrected.cool \
    -o ../figures/bowtie2/local/normalized/normsm_filter_pooled_40kb_corrected_chr12-60-70Mb.png \
    --region chr12:60000000-70000000 --log1p \
    --colorMap "Reds" &

wait

INFO:hicexplorer.hicPlotMatrix:Cooler or no cooler: True
INFO:hicexplorer.hicPlotMatrix:Cooler or no cooler: True
INFO:hicexplorer.hicPlotMatrix:Cooler or no cooler: True

from hicstuff import plot_pngs_in_grid as plt

plt("../figures/bowtie2/local/normalized/", suffix="corrected_chr12*.png", ncol=3)

Plotting all images in '../figures/bowtie2/local/normalized/*corrected_chr12*.png':

ChrX

%%bash 

hicPlotMatrix \
    -m ../steps/bowtie2/local/matrices/normsm_filtered_pooled_100kb_corrected.cool \
    -o ../figures/bowtie2/local/normalized/normsm_filter_pooled_100kb_corrected_chrX-1-105Mb.png \
    -t 'ChrX: 100kb bins' \
    --region chrX:1-105000000 --log1p \
    --colorMap "Reds" &

hicPlotMatrix \
    -m ../steps/bowtie2/local/matrices/normsm_filtered_pooled_50kb_corrected.cool \
    -o ../figures/bowtie2/local/normalized/normsm_filter_pooled_50kb_corrected_chrX-60-70Mb.png \
    -t 'ChrX: 50kb bins' \
    --region chrX:60000000-70000000 --log1p \
    --colorMap "Reds" &

hicPlotMatrix \
    -m ../steps/bowtie2/local/matrices/normsm_filtered_pooled_40kb_corrected.cool \
    -o ../figures/bowtie2/local/normalized/normsm_filter_pooled_40kb_corrected_chrX-60-70Mb.png \
    -t 'ChrX: 40kb bins' \
    --region chrX:60000000-70000000 --log1p \
    --colorMap "Reds" &

wait

INFO:hicexplorer.hicPlotMatrix:Cooler or no cooler: True
INFO:hicexplorer.hicPlotMatrix:Cooler or no cooler: True
INFO:hicexplorer.hicPlotMatrix:Cooler or no cooler: True

from hicstuff import plot_pngs_in_grid as plt

plt("../figures/bowtie2/local/normalized/", suffix="corrected_chrX*.png", ncol=3)

Plotting all images in '../figures/bowtie2/local/normalized/*corrected_chrX*.png':

%%bash

hicPlotMatrix \
    -m ../steps/bowtie2/local/matrices/normsm_filtered_pooled_100kb_corrected.cool \
    -o ../figures/bowtie2/local/normalized/normsm_filter_pooled_100kb_corrected_chrX-full.png \
    --chromosomeOrder chrX \
    --dpi 320 \
    --colorMap "Reds" \
    --log1p \
    --increaseFigureWidth 0 \
    --increaseFigureHeight 0

INFO:hicexplorer.hicPlotMatrix:Cooler or no cooler: True

from hicstuff import plot_pngs_in_grid as plt

plt("../figures/bowtie2/local/normalized/", suffix="normsm*corrected_chrX*.png", ncol=2)

Dist versus counts (P(s) in Wang2019?)

!hicPlotDistVsCounts --help

usage: hicPlotDistVsCounts --matrices MATRICES [MATRICES ...] --plotFile file
                           name [--labels LABELS [LABELS ...]]
                           [--skipDiagonal] [--maxdepth INT bp] [--perchr]
                           [--chromosomeExclude CHROMOSOMEEXCLUDE [CHROMOSOMEEXCLUDE ...]]
                           [--domains DOMAINS] [--outFileData OUTFILEDATA]
                           [--plotsize PLOTSIZE PLOTSIZE] [--help] [--version]

This program creates distance vs. Hi-C counts plots. It can use several matrix
files to compare them at once. If the `--perchr` option is given, each
chromosome is plotted independently. When plotting multiple matrices, denser
matrices are scaled down to match the sum of the smallest matrix.

Required arguments:
  --matrices MATRICES [MATRICES ...], -m MATRICES [MATRICES ...]
                        Hi-C normalized (corrected) matrices. Each path should
                        be separated by a space.
  --plotFile file name, -o file name
                        File name to save the file. The given file ending will
                        be used to determine the image format. The available
                        options are: .png, .emf, .eps, .pdf and .svg.

Optional arguments:
  --labels LABELS [LABELS ...]
                        Label to assign to each matrix file. Each label should
                        be separated by a space. Quote labels that contain
                        spaces: E.g. --labels label1 "labels 2". If no labels
                        are given then the file name is used.
  --skipDiagonal, -s    If set, diagonal counts are not included.
  --maxdepth INT bp     Maximum distance from diagonal to use. In other words,
                        distances up to maxDepth are computed. Default is 3
                        million bp.
  --perchr              If given, computes and display distance versus Hi-C
                        counts plots for each chromosome stored in the
                        matrices passed to --matrices.
  --chromosomeExclude CHROMOSOMEEXCLUDE [CHROMOSOMEEXCLUDE ...]
                        Exclude the given list of chromosomes. This is useful
                        for example to exclude the Y chromosome. The names of
                        the chromosomes should be separated by space.
  --domains DOMAINS     Bed file with domains coordinates: instead of
                        evaluating the distance vs. Hi-C counts for intra
                        chromosomal counts, compute it for intra-domains.
  --outFileData OUTFILEDATA
                        If given, the data underlying the plots is saved on
                        this file.
  --plotsize PLOTSIZE PLOTSIZE
                        Width and height of the plot (in inches). Default is
                        6*number of cols, 4 * number of rows. The maximum
                        number of rows is 4. Example: --plotsize 6 5
  --help, -h            show this help message and exit
  --version             show program's version number and exit

%%bash 

hicPlotDistVsCounts \
    -m ../steps/bowtie2/local/matrices/normsm_filtered_pooled_100kb_corrected.cool \
    -o ../figures/bowtie2/local/normalized/distvscounts_100kb_corrected_chr.png \
    --perchr \
    --labels 'Pooled' \
    --plotsize 6 4 &

hicPlotDistVsCounts \
    -m ../steps/bowtie2/local/matrices/normsm_filtered_pooled_100kb_corrected.cool \
    -o ../figures/bowtie2/local/normalized/distvscounts_100kb_corrected_all.png \
    --labels 'Pooled' \
    --plotsize 6 4 &

wait

INFO:hicexplorer.hicPlotDistVsCounts:processing chromosome all

INFO:hicexplorer.hicPlotDistVsCounts:processing chromosome chr1

INFO:hicexplorer.hicPlotDistVsCounts:processing chromosome chr2

INFO:hicexplorer.hicPlotDistVsCounts:processing chromosome chr3

INFO:hicexplorer.hicPlotDistVsCounts:zero value for 47, diagonal len: 1791

INFO:hicexplorer.hicPlotDistVsCounts:processing chromosome chr4

INFO:hicexplorer.hicPlotDistVsCounts:processing chromosome chr5

INFO:hicexplorer.hicPlotDistVsCounts:processing chromosome chr6

INFO:hicexplorer.hicPlotDistVsCounts:zero value for 49, diagonal len: 1724

INFO:hicexplorer.hicPlotDistVsCounts:zero value for 50, diagonal len: 1723

INFO:hicexplorer.hicPlotDistVsCounts:processing chromosome chr7

INFO:hicexplorer.hicPlotDistVsCounts:processing chromosome chr8

INFO:hicexplorer.hicPlotDistVsCounts:processing chromosome chr9

INFO:hicexplorer.hicPlotDistVsCounts:zero value for 48, diagonal len: 1265

INFO:hicexplorer.hicPlotDistVsCounts:zero value for 49, diagonal len: 1264

INFO:hicexplorer.hicPlotDistVsCounts:zero value for 50, diagonal len: 1263

INFO:hicexplorer.hicPlotDistVsCounts:zero value for 51, diagonal len: 1262

INFO:hicexplorer.hicPlotDistVsCounts:zero value for 52, diagonal len: 1261

INFO:hicexplorer.hicPlotDistVsCounts:zero value for 53, diagonal len: 1260

INFO:hicexplorer.hicPlotDistVsCounts:zero value for 54, diagonal len: 1259

INFO:hicexplorer.hicPlotDistVsCounts:zero value for 55, diagonal len: 1258

INFO:hicexplorer.hicPlotDistVsCounts:zero value for 56, diagonal len: 1257

INFO:hicexplorer.hicPlotDistVsCounts:zero value for 57, diagonal len: 1256

INFO:hicexplorer.hicPlotDistVsCounts:zero value for 58, diagonal len: 1255

INFO:hicexplorer.hicPlotDistVsCounts:zero value for 59, diagonal len: 1254

INFO:hicexplorer.hicPlotDistVsCounts:skipping rest of chromosome chr9. Too many emtpy diagonals

INFO:hicexplorer.hicPlotDistVsCounts:processing chromosome chr10

INFO:hicexplorer.hicPlotDistVsCounts:zero value for 48, diagonal len: 908

INFO:hicexplorer.hicPlotDistVsCounts:zero value for 49, diagonal len: 907

INFO:hicexplorer.hicPlotDistVsCounts:zero value for 50, diagonal len: 906

INFO:hicexplorer.hicPlotDistVsCounts:zero value for 51, diagonal len: 905

INFO:hicexplorer.hicPlotDistVsCounts:zero value for 52, diagonal len: 904

INFO:hicexplorer.hicPlotDistVsCounts:zero value for 53, diagonal len: 903

INFO:hicexplorer.hicPlotDistVsCounts:zero value for 54, diagonal len: 902

INFO:hicexplorer.hicPlotDistVsCounts:zero value for 55, diagonal len: 901

INFO:hicexplorer.hicPlotDistVsCounts:zero value for 56, diagonal len: 900

INFO:hicexplorer.hicPlotDistVsCounts:zero value for 57, diagonal len: 899

INFO:hicexplorer.hicPlotDistVsCounts:zero value for 58, diagonal len: 898

INFO:hicexplorer.hicPlotDistVsCounts:zero value for 59, diagonal len: 897

INFO:hicexplorer.hicPlotDistVsCounts:skipping rest of chromosome chr10. Too many emtpy diagonals

INFO:hicexplorer.hicPlotDistVsCounts:processing chromosome chr11

INFO:hicexplorer.hicPlotDistVsCounts:processing chromosome chr12

INFO:hicexplorer.hicPlotDistVsCounts:processing chromosome chr13

INFO:hicexplorer.hicPlotDistVsCounts:The scale factors used are: {'../steps/bowtie2/local/matrices/normsm_filtered_pooled_100kb_corrected.cool': 1.0}
INFO:hicexplorer.hicPlotDistVsCounts:processing chromosome chr14

INFO:hicexplorer.hicPlotDistVsCounts:processing chromosome chr15

INFO:hicexplorer.hicPlotDistVsCounts:processing chromosome chr16

INFO:hicexplorer.hicPlotDistVsCounts:processing chromosome chr17

INFO:hicexplorer.hicPlotDistVsCounts:processing chromosome chr18

INFO:hicexplorer.hicPlotDistVsCounts:processing chromosome chr19

INFO:hicexplorer.hicPlotDistVsCounts:processing chromosome chr20

INFO:hicexplorer.hicPlotDistVsCounts:processing chromosome chrX

INFO:hicexplorer.hicPlotDistVsCounts:processing chromosome chrY

INFO:hicexplorer.hicPlotDistVsCounts:The scale factors used are: {'../steps/bowtie2/local/matrices/normsm_filtered_pooled_100kb_corrected.cool': 1.0}

from hicstuff import plot_pngs_in_grid as plt

plt("../figures/bowtie2/local/normalized/", suffix="distvscounts*.png", ncol=2)

Plotting all images in '../figures/bowtie2/local/normalized/*distvscounts*.png':

Chromatin Compartments

HiCExplorer

!hicPCA --help

usage: hicPCA --matrix MATRIX --outputFileName OUTPUTFILENAME
              [OUTPUTFILENAME ...]
              [--whichEigenvectors WHICHEIGENVECTORS [WHICHEIGENVECTORS ...]]
              [--format {bedgraph,bigwig}]
              [--chromosomes CHROMOSOMES [CHROMOSOMES ...]]
              [--method {dist_norm,lieberman}] [--ligation_factor]
              [--extraTrack EXTRATRACK] [--histonMarkType HISTONMARKTYPE]
              [--pearsonMatrix PEARSONMATRIX] [--obsexpMatrix OBSEXPMATRIX]
              [--ignoreMaskedBins] [--help] [--version]

Computes PCA eigenvectors for a Hi-C matrix.

    $ hicPCA --matrix hic_matrix.h5 -o pca1.bedgraph pca2.bedgraph

Required arguments:
  --matrix MATRIX, -m MATRIX
                        HiCExplorer matrix in h5 format. (default: None)
  --outputFileName OUTPUTFILENAME [OUTPUTFILENAME ...], -o OUTPUTFILENAME [OUTPUTFILENAME ...]
                        File names for the result of the pca.Number of output
                        files must match the number of computed eigenvectors.
                        (default: None)

Optional arguments:
  --whichEigenvectors WHICHEIGENVECTORS [WHICHEIGENVECTORS ...], -we WHICHEIGENVECTORS [WHICHEIGENVECTORS ...]
                        The list of eigenvectors that the PCA should compute
                        e.g. 1 2 5 will return the first, second and fifth
                        eigenvector. (Default: 1 2).
  --format {bedgraph,bigwig}, -f {bedgraph,bigwig}
                        Output format. Either bedgraph or bigwig (Default:
                        bigwig).
  --chromosomes CHROMOSOMES [CHROMOSOMES ...]
                        List of chromosomes to be included in the correlation.
                        (default: None)
  --method {dist_norm,lieberman}
                        possible methods which can be used to build the obs-
                        exp matrix are dist_norm and lieberman (Default:
                        dist_norm).
  --ligation_factor     Setting this flag multiplies a scaling factor to each
                        entry of the expected matrix to take care of the
                        proximity ligation as has been explained in Homer
                        software. This flag is only affective with dist_norm
                        method and will be ignored if lieberman method is
                        chosen. (default: False)
  --extraTrack EXTRATRACK
                        Either a gene track or a histone mark coverage file
                        (preferably a broad mark) is needed to decide if the
                        values of the eigenvector need a sign flip or not.
                        Please consider: bed files are interpreted as gene
                        tracks and bigwig files as histone marks. (default:
                        None)
  --histonMarkType HISTONMARKTYPE
                        Set it to active or inactive. This is only necessary
                        if a histon mark coverage file is given as an
                        extraTrack (Default: active).
  --pearsonMatrix PEARSONMATRIX, -pm PEARSONMATRIX
                        Internally the input matrix is converted per
                        chromosome to obs_exp matrix and consecutively to a
                        Pearson matrix. Set this parameter to write the
                        pearson matrix to a file. (default: None)
  --obsexpMatrix OBSEXPMATRIX, -oem OBSEXPMATRIX
                        Internally the input matrix is converted per
                        chromosome to obs_exp matrix and consecutively to a
                        Pearson matrix. Set this parameter to write the
                        observe/expected matrix to a file. (default: None)
  --ignoreMaskedBins    Mask bins are usually set to 0. This option removes
                        the masked bins before the PCA is computed. Attention:
                        this will lead to empty PCA regions. (default: False)
  --help, -h            show the help message and exit
  --version             show program's version number and exit

%%bash

hicPCA \
    -m ../steps/bowtie2/local/matrices/normsm_filtered_pooled_100kb_corrected.cool \
    -o ../figures/bowtie2/local/normalized/pc{1,2,3}_100kb_corrected_chrX.bigwig \
    --chromosomes chrX \
    -we 1 2 3 &

hicPCA \
    -m ../steps/bowtie2/local/matrices/normsm_filtered_pooled_50kb_corrected.cool \
    -o ../figures/bowtie2/local/normalized/pc{1,2,3}_50kb_corrected_chrX.bigwig \
    --chromosomes chrX \
    -we 1 2 3 &

wait

%%bash 

for NUM in 1 2 3; do
hicPlotMatrix \
    -m ../steps/bowtie2/local/matrices/normsm_filtered_pooled_50kb_corrected.cool \
    -o ../figures/bowtie2/local/normalized/pc${NUM}_50kb_corrected_chrX.png \
    --bigwig ../figures/bowtie2/local/normalized/pc${NUM}_50kb_corrected_chrX.bigwig \
    --region chrX \
    -t "ChrX:50kb bins: PC${NUM}" \
    --log1p \
    --colorMap "Reds" \
    --dpi 100 &
done

wait

INFO:hicexplorer.hicPlotMatrix:Cooler or no cooler: True
INFO:hicexplorer.hicPlotMatrix:Cooler or no cooler: True
INFO:hicexplorer.hicPlotMatrix:Cooler or no cooler: True

import hicstuff
import importlib
importlib.reload(hicstuff)
from hicstuff import plot_pngs_in_grid as plt

plt("../figures/bowtie2/local/normalized", suffix="pc*50kb*chrX.png", ncol=3)

The X chromosome in 50kb bins and the first 3 PCs below. Made with HicExplorer.

import hicstuff
import importlib
importlib.reload(hicstuff)
from hicstuff import plot_pngs_in_grid as plt

plt("../figures/bowtie2/local/normalized", suffix="pc*100kb*chrX.png", ncol=3)

The X chromosome in 100kb bins and the first 3 PCs below. Made with HicExplorer.

matplotlib

[f"../figures/bowtie2/local/normalized/pc{NUM}_50kb_corrected_chrX.bigwig" for NUM in range(1,4)]

['../figures/bowtie2/local/normalized/pc1_50kb_corrected_chrX.bigwig',
 '../figures/bowtie2/local/normalized/pc2_50kb_corrected_chrX.bigwig',
 '../figures/bowtie2/local/normalized/pc3_50kb_corrected_chrX.bigwig']

import h5py
import pyBigWig
import matplotlib.pyplot as plt
import numpy as np

# Load Hi-C matrix from .cool file
cool_file = '../steps/bowtie2/local/matrices/normsm_filtered_pooled_100kb_corrected.cool'
f = h5py.File(cool_file, 'r')

for key in list(f.keys()):
    print(f"{key}: {list(f[key])}")

bins: ['chrom', 'end', 'start', 'weight']
chroms: ['length', 'name']
indexes: ['bin1_offset', 'chrom_offset']
pixels: ['bin1_id', 'bin2_id', 'count']

bins = f['bins']
chroms = f['chroms']
indexes = f['indexes']
pixels = f['pixels']

# Determine the size of the matrix
num_bins = len(bins['start'])
hic_matrix = np.zeros((num_bins, num_bins))

# NB Uses 20Gb RAM
# Fill the Hi-C matrix using pixels and indexes
bin1_ids = pixels['bin1_id']
bin2_ids = pixels['bin2_id']
counts = np.log1p(pixels['count'])  # Apply log1p transformation directly

# Use NumPy's advanced indexing to fill the matrix
hic_matrix[bin1_ids, bin2_ids] = counts
hic_matrix[bin2_ids, bin1_ids] = counts  # Symmetric matrix

# NB Uses 32 Gb RAM
# Load bw files

bw_files = [f"../figures/bowtie2/local/normalized/pc{NUM}_100kb_corrected_chrX.bigwig" for NUM in range(1,4)]
bw_data = []
for bw_file in bw_files:
    bw = pyBigWig.open(bw_file)
    chroms = bw.chroms()
    data = []
    for chrom in chroms:
        chrom_data = bw.values(chrom, 0, chroms[chrom])
        data.append(chrom_data)
    bw_data.append(np.concatenate(data))
    bw.close()

# NB Crashed at 64 Gb RAM w/ 50 kb bins

# Plot Hi-C matrix
fig, ax = plt.subplots(len(bw_files) + 1, 1, figsize=(10, 10), gridspec_kw={'height_ratios': [3] + [1] * len(bw_files)})

# Plot Hi-C matrix with log1p transformation
ax[0].imshow(hic_matrix_dense, cmap='Reds', aspect='equal')
ax[0].set_title('Hi-C Matrix (log1p transformed)')

# Plot bigwig tracks
for i, data in enumerate(bw_data):
    ax[i + 1].plot(data)
    ax[i + 1].set_title(f'PC{i + 1}')
    ax[i + 1].set_xlim(0, len(data))

plt.tight_layout()
plt.show()

First try Copilot

I don´t want to spend more time on this now. Switching notebook to cooler.

import h5py
import pyBigWig
import matplotlib.pyplot as plt
import numpy as np
import scipy.sparse as sp
import gc

# Load Hi-C matrix from .cool file
cool_file = '../steps/bowtie2/local/matrices/normsm_filtered_pooled_100kb_corrected.cool'

with h5py.File(cool_file, 'r') as f:
    bins = f['bins']
    pixels = f['pixels']

    # Determine the size of the matrix
    num_bins = len(bins['start'])
    hic_matrix = sp.lil_matrix((num_bins, num_bins))

    # Fill the Hi-C matrix using pixels
    bin1_ids = pixels['bin1_id']
    bin2_ids = pixels['bin2_id']
    counts = np.log1p(pixels['count'])  # Apply log1p transformation directly

    # Use sparse matrix to fill the matrix
    hic_matrix[bin1_ids, bin2_ids] = counts
    hic_matrix[bin2_ids, bin1_ids] = counts  # Symmetric matrix

# Convert to CSR format for efficient arithmetic and matrix vector operations
hic_matrix = hic_matrix.tocsr()

# Load bw files and plot in chunks
bw_files = [f"../figures/bowtie2/local/normalized/pc{NUM}_100kb_corrected_chrX.bigwig" for NUM in range(1, 4)]

fig, ax = plt.subplots(len(bw_files) + 1, 1, figsize=(10, 10), gridspec_kw={'height_ratios': [3] + [1] * len(bw_files)})

# Plot Hi-C matrix with log1p transformation
ax[0].imshow(hic_matrix.toarray(), cmap='Reds', aspect='equal')
ax[0].set_title('Hi-C Matrix (log1p transformed)')

# Plot bigwig tracks
for i, bw_file in enumerate(bw_files):
    with pyBigWig.open(bw_file) as bw:
        chroms = bw.chroms()
        data = []
        for chrom in chroms:
            chrom_data = bw.values(chrom, 0, chroms[chrom])
            data.append(chrom_data)
        data = np.concatenate(data)
        ax[i + 1].plot(data)
        ax[i + 1].set_title(f'PC{i + 1}')
        ax[i + 1].set_xlim(0, len(data))

plt.tight_layout()
plt.show()

# Free memory
del hic_matrix
del data
gc.collect()

9