Part 1: Bash Script for Bedtools Commands (2.5 pts)
Your script correctly processes the input files by sorting and merging the feature files. You also implemented the correct method for subtracting exonic, intronic, and cCRE regions to create the "other" bed file.
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, using loops to iterate over both MAF values and genomic features. The calculations for SNP density and enrichment are correct, and the results are written to the output file in the correct format.
Score: 4.5/4.5
2.2 Text File with SNP Enrichments (0.5 pts)
Your snp_counts.txt file is formatted correctly and includes the required MAF-feature combinations. The enrichment values are accurate and match the reference closely.
Score: 0.5/0.5
2.3 Plot from Step 2.4 (1.5 pts)
Your plot is clear and follows the correct log2 transformation. The lines for each feature are distinguishable, and the labels on both axes are appropriate. The plot title is informative, and the trends align with expectations.
Score: 1.5/1.5
2.4 Answers to Questions in README.md (1.0 pts)
Your answers to the questions demonstrate a good understanding of the concepts. You correctly identified exons as being under the highest purifying selection, and your explanation of SNP enrichment at different MAF levels is solid.
Part 1: Bash Script for Bedtools Commands (2.5 pts)
Your script correctly processes the input files by sorting and merging the feature files. You also implemented the correct method for subtracting exonic, intronic, and cCRE regions to create the "other" bed file.
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, using loops to iterate over both MAF values and genomic features. The calculations for SNP density and enrichment are correct, and the results are written to the output file in the correct format.
Score: 4.5/4.5
2.2 Text File with SNP Enrichments (0.5 pts)
Your
snp_counts.txtfile is formatted correctly and includes the required MAF-feature combinations. The enrichment values are accurate and match the reference closely.Score: 0.5/0.5
2.3 Plot from Step 2.4 (1.5 pts)
Your plot is clear and follows the correct log2 transformation. The lines for each feature are distinguishable, and the labels on both axes are appropriate. The plot title is informative, and the trends align with expectations.
Score: 1.5/1.5
2.4 Answers to Questions in README.md (1.0 pts)
Your answers to the questions demonstrate a good understanding of the concepts. You correctly identified exons as being under the highest purifying selection, and your explanation of SNP enrichment at different MAF levels is solid.
Score: 1.0/1.0
Total Score: 10/10
Final Comments:
Excellent work overall!