Week 2 Assignment - Githubissues

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

Your script correctly implements the necessary bedtools commands for sorting, merging, and subtracting the feature files. You followed the expected workflow for creating the exon, intron, and "other" bed files. Overall, this part is well done.

Score: 2.5/2.5

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

2.1 Shell Script for Calculating Enrichments (0.0 pts)

The shell script provided only includes the commands for processing feature files from Part 1. There is no implementation of SNP enrichment calculations using bedtools coverage.

Score: 0.0/4.5

2.2 Text File with SNP Enrichments (0.25 pts)

Your snp_counts.txt file is included but incomplete. The "other" feature is missing values across all MAFs.

Score: 0.25/0.5

2.3 Plot from Step 2.4 (1.25 pts)

The plot is mostly clear and follows the correct log2 transformation. The x- and y-axis labels are correct, but the y-axis values for enrichment appear unusually low, especially for exons and cCREs, which may indicate an issue in the underlying SNP calculations.

Score: 1.25/1.5

2.4 Answers to Questions in README.md (0 pts)

No README file was provided.

Score: 0.0/1.0

Total Score: 4.0/10

Final Comments:

While the feature processing in Part 1 is solid, the lack of SNP enrichment calculations and the incomplete snp_counts.txt file significantly affect the overall score. In future assignments, make sure to check the rubric and push all necessary files!. COME TO OFFICE HOURS IF YOU NEED HELP!!

saraseegers / qbb2024-answers

Week 2 Assignment #9