Week 2 Assignment

[jonathanfischer97]

Part 1: Bash Script for Bedtools Commands (2.5 pts)

You did not submit the shell script for creating the feature bed files using bedtools. This was required to get full credit for Part 1.

Score: 0/2.5

Part 2: SNP Enrichment Calculation and Analysis (7.5 pts)

2.1 Shell Script for Calculating Enrichments (4.5 pts)

Your script correctly implements the logic to calculate SNP enrichments across different MAF levels and genomic features. The loops, use of bedtools, and calculations with awk and bc are accurate.

Score: 4.5/4.5

2.2 Text File with SNP Enrichments (0.5 pts)

Score: 0.5/0.5

2.3 Plot from Step 2.4 (1.5 pts)

Your plot is clear, with correctly calculated log2-transformed SNP enrichment values. The lines for each feature are distinguishable, and the trends are biologically accurate.

Score: 1.5/1.5

2.4 Answers to Questions in README.md (1.0 pts)

Your answers demonstrate a understanding but lack details:

• In discussing purifying selection, you correctly identified exons but did not explain the selective pressures in enough detail.
• Your explanation of why features are more enriched at lower MAFs is unclear and does not mention how natural selection impacts recent vs. older mutations.
• Your discussion of the relative levels of enrichment/depletion across features misses important details about the varying functional constraints on regions like introns and cCREs.

Score: 0.5/1.0

Total Score: 7/10

[mcrott]

Updated with revisions.

[jonathanfischer97]

Week 2 Regrade

• Included the Part 1 bash script, +2.5 points
• Better answers in the README, but was looking for a mention of the relative differences between each of the feature classes, not just the exons versus everything else. +0.25 points

Total score: 9.75 points

Good job!