Work plan

Schedule / Work plan

Semester: Monday, Aug 26th – Wednesday, Jan 15th (Week 35-3)
Hand-in: Wednesday, Jan 15th (Week 3)
Holiday: Wednesday, Oct 23rd – Monday, Oct 28th (Week 43)
Christmas Holidays: Monday, Dec 23rd – Friday, Jan 3rd (Week 52-1)

Week 35-36 (Aug 26 - Sep 7):
Conduct a literature review on chromatin architecture, Hi-C methodology, and the concept of selfish genes. Get an overview of (and obtain) data sets to be used.

Week 37-38 (Sep 9 - Sep 21):
Assess the status of existing Hi-C data (raw or QC’ed). If necessary, perform initial quality control. Align reads to reference genomes.

Week 39-40 (Sep 23 - Oct 5):
Process Hi-C interaction data. Perform quality assessment.

Week 41-42 (Oct 7 - Oct 19):
Generate and normalize interaction matrices for the X chromosome.

Week 43 (Oct 21 - Oct 26):
Holiday from Wednesday (no major activities planned). Tidy notes and do some writing.

Week 44-45 (Oct 28 - Nov 9):
Perform PCA to obtain PC1 compartments. Visualize results.

Week 46-47 (Nov 11 - Nov 23):
Identify A/B compartment transitions. Overlay with positive selection regions.

Week 48-49 (Nov 25 - Dec 7):
Conduct cross-species analysis by converting genomic coordinates.

Week 50 (Dec 9 - Dec 14):
Finish analyses. Compare results.

Week 51 (Dec 16 - Dec 21):
Finalize analyses and begin writing initial thesis draft, incorporating analysis results and discussions.

Week 52 (Dec 23 - Dec 28):
Christmas holidays (no major activities planned). Will work a couple of days Dec 27-29.

Week 1 (Dec 30 - Jan 4):
Christmas holidays until Jan 2 (just performing modifications to analyses, etc.).

Week 2 (Jan 6 - Jan 11):
Revise thesis draft based on feedback. Continue refinement of analyses if necessary.

Week 3 (Jan 13 - Jan 15):
Final revisions and hand-in on Wednesday, January 15th.