Fibroblasts_all.dedup
A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.
Report generated on 2024-10-07, 13:37 CEST based on data in:
/faststorage/project/hic-spermatogenesis/people/sojern/hic-spermatogenesis/steps/bwa/PE/pairs/SRR6502335.dedup.stats/faststorage/project/hic-spermatogenesis/people/sojern/hic-spermatogenesis/steps/bwa/PE/pairs/SRR6502336.dedup.stats/faststorage/project/hic-spermatogenesis/people/sojern/hic-spermatogenesis/steps/bwa/PE/pairs/SRR6502337.dedup.stats/faststorage/project/hic-spermatogenesis/people/sojern/hic-spermatogenesis/steps/bwa/PE/pairs/SRR6502338.dedup.stats/faststorage/project/hic-spermatogenesis/people/sojern/hic-spermatogenesis/steps/bwa/PE/pairs/SRR6502339.dedup.stats
General Statistics
| Sample Name | Read pairs | Unmapped | One-sided | Two-sided | Duplicated | Unique pairs | Cis |
|---|---|---|---|---|---|---|---|
| SRR6502335 | 244.0M | 26.8% | 17.7% | 55.5% | 8.0% | 115.9M | 78.4% |
| SRR6502336 | 217.1M | 27.2% | 16.9% | 55.9% | 10.5% | 98.6M | 78.5% |
| SRR6502337 | 175.9M | 27.8% | 17.8% | 54.5% | 7.3% | 82.9M | 76.5% |
| SRR6502338 | 174.6M | 27.2% | 17.2% | 55.6% | 4.9% | 88.5M | 76.5% |
| SRR6502339 | 96.3M | 27.9% | 16.7% | 55.4% | 11.2% | 42.5M | 76.5% |
pairtools
Toolkit for Chromatin Conformation Capture experiments. Handles short-reads paired reference alignments, extracts 3C-specific information, and perform common tasks such as sorting, filtering, and deduplication.URL: https://github.com/mirnylab/pairtoolsDOI: 10.5281/zenodo.1490830; 10.1101/2023.02.13.528389
Pairs by alignment status
Number of pairs classified according to their alignment status, including uniquely mapped (UU), unmapped (NN), duplicated (DD), and others.
For further details check pairtools documentation.
Pre-filtered pairs by genomic location (overview)
Distribution of pre-filtered pairs (mapping uniquely and rescued) by genomic separation for
Samples can have different distributions of pairs by genomic locations for various biological and technical reasons. Biological examples: cell-cycle stages, differentitation stages difference, mutations affecting genome organization, etc. Technical differences arise due to the fact that pre-filtered read pairs still include artifacts: Short-range cis-pairs (<1kb) are typically enriched in ligation artifacts (self-circles, dangling-ends, etc). Elevated number of trans interactions typically suggests increased noise levels - e.g. random ligations etc.
Pre-filtered pairs as a function of genomic separation (in detail)
Number of interactions (pre-filtered pairs) as a function of genomic separation, log-binned. Click on an individual curve to reveal information for different read pair orientations.
Short-range cis-pairs are typically enriched in ligation artifacts. Frequency of interactions for read pairs of different orientations ++,+-,-+ and -- (FF, FR, RF, RR) provide insight into these artifacts. For example, dangling-ends manifest themselves as FR-pairs, while self-circles - RF. Thus, enrichment of FR/RF pairs at a given genomic separation can hint at the level of contamination.
Fraction of read pairs by strand orientation
Number of pre-filtered pairs reported for every type of read pair orientation. Numbers are reported for different ranges of genomic separation and combined.
Short-range cis-pairs are typically enriched in technical artifacts. Frequency of interactions for read pairs of different orientations ++,+-,-+ and -- (FF, FR, RF, RR) provide insight into these technical artifacts. For example, dangling-ends manifest themselves as FR-pairs, while self-circles - RF. Thus, enrichment of FR/RF pairs at a given genomic separation can hint at the level of contamination.
