Part 2: SNP Enrichment Calculation and Analysis (7.5 pts)
2.1 Shell Script for Calculating Enrichments (4.5 pts)
Your shell script is well-structured and correctly calculates SNP enrichments using bedtools coverage, awk, and bc. The loop structure and calculations are correctly implemented, and the results are saved to the output file as expected.
Score: 4.5/4.5
2.2 Text File with SNP Enrichments (0.5 pts)
Your snp_counts.txt file is included and contains the necessary MAF-feature combinations with accurate enrichment values. The file is formatted correctly and matches the expected results.
Score: 0.5/0.5
2.3 Plot from Step 2.4 (1.25 pts)
The plot is provided and follows the correct log2 transformation of SNP enrichment values. However, the y-axis values are small for some features, and the trends are not as pronounced as expected.
Score: 1.25/1.5
2.4 Answers to Questions in README.md (0 pts)
No README file was pushed.
Score: 0.0/1.0
Total Score: 6.25/10
Final Comments:
Your implementation of the SNP enrichment calculations is solid, and the results in the SNP counts file are correct. However, the lack of a script for Part 1 and the absence of a README file impact the overall score. In future assignments, be sure to include all required components from the rubric!
Part 1: Bash Script for Bedtools Commands (0 pts)
No script for Part 1 was pushed.
Score: 0.0/2.5
Part 2: SNP Enrichment Calculation and Analysis (7.5 pts)
2.1 Shell Script for Calculating Enrichments (4.5 pts)
Your shell script is well-structured and correctly calculates SNP enrichments using
bedtools coverage,awk, andbc. The loop structure and calculations are correctly implemented, and the results are saved to the output file as expected.Score: 4.5/4.5
2.2 Text File with SNP Enrichments (0.5 pts)
Your
snp_counts.txtfile is included and contains the necessary MAF-feature combinations with accurate enrichment values. The file is formatted correctly and matches the expected results.Score: 0.5/0.5
2.3 Plot from Step 2.4 (1.25 pts)
The plot is provided and follows the correct log2 transformation of SNP enrichment values. However, the y-axis values are small for some features, and the trends are not as pronounced as expected.
Score: 1.25/1.5
2.4 Answers to Questions in README.md (0 pts)
No README file was pushed.
Score: 0.0/1.0
Total Score: 6.25/10
Final Comments:
Your implementation of the SNP enrichment calculations is solid, and the results in the SNP counts file are correct. However, the lack of a script for Part 1 and the absence of a README file impact the overall score. In future assignments, be sure to include all required components from the rubric!