Week 2 Assignment

[jonathanfischer97]

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

Your script correctly implements the necessary bedtools commands for sorting, merging, and subtracting the various feature files. You used bedtools to create the exon, intron, and "other" bed files efficiently and covered all the necessary steps.

Score: 2.5/2.5

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

2.1 Shell Script for Calculating Enrichments (4.5 pts)

Your script is well-structured and correctly loops through the MAF and feature files, calculating the necessary SNP enrichments using bedtools. You used awk and bc to compute SNP counts and densities effectively, and your logic for calculating enrichment is accurate. The results were written to snp_counts.txt in the correct format.

Score: 4.5/4.5

2.2 Text File with SNP Enrichments (0.5 pts)

You did not submit the required text file with SNP enrichments (e.g., snp_counts.txt), so no points can be awarded for this part.

Score: 0/0.5

2.3 Plot from Step 2.4 (1.5 pts)

Your plot shows the correct features (cCREs, exons, introns, and other) against MAF values. However, you applied the log2 transformation incorrectly by using scale_y_continuous(trans="log2") in ggplot2. The correct approach is to apply the log2() transformation to the data itself before plotting. True plot should look like this, notice the y-axis:

Score: 0.75/1.5

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

Score: 1.0/1.0

Total Score: 8.75/10

[jonathanfischer97]

Week 2 Regrade

• Included txt file, +0.5 points.
• Looks like the .png is your new plot, but it's all squished and doesn't actually show anything! Don't know if you looked at it before you submitted, but make sure to double check any plots you produce before pushing. Sometimes formatting things can get in the way, and since I can't see anything on the plot, can't award any additional points.

Total score: 9.25 points

Great job nonetheless!