jonathanfischer97
commented
1 week ago Week 2 Regrade
- Part 1 script included, 2.5/2.5. +0.25 pts
- Part 2 script looks good, +4.5 points
- Text file include, +0.5 points
- Plot looks good, +1.5 points
- README answers are better, but in Q2 still failed to explain how natural selection over time would reduce enrichment at higher MAF values due to purifying selection on deleterious variants. Interesting thoughts about redundancy and compensation though. In Q3, could have used more elaboration on the relative enrichment trajectories of each feature class, i.e why exons are lower than introns and cCREs, and why cCREs are lower than introns. Will give you 0.9/10, as it seems you understand the concepts, but next time just make sure you are answering the question fully! +0.15 points
Total score: 9.9/10
Good job Etta!
Part 1: Bash Script for Bedtools Commands (2.5 pts)
The bash commands in your README file are correct. But put these in their own
.shbash script next time, as the rubric asked for.Score: 2.25/2.5
Part 2: SNP Enrichment Calculation and Analysis (7.5 pts)
2.1 Shell Script for Calculating Enrichments (0.0 pts)
Your script is incomplete. The
forloop and bedtools commands are not fully implemented, and it appears that the script ends prematurely without processing the SNP files or calculating SNP enrichments.Score: 0.0/4.5
2.2 Text File with SNP Enrichments (0 pts)
No SNP enrichment text file was pushed.
Score: 0.0/0.5
2.3 Plot from Step 2.4 (0 pts)
No plot was pushed.
Score: 0.0/1.5
2.4 Answers to Questions in README.md (0.75 pts)
Your answers in the README.md file touch on the key concepts but lack depth. While you identified exons as being under the highest purifying selection, your explanations for MAF trends and the selective pressures across features could be more detailed. Also, please ensure your answers address the biological mechanisms driving the differences in SNP density and selection across regions.
Score: 0.75/1.0
Total Score: 3.0/10
Final Comments:
While your commands for Part 1 is correct, the incomplete Part 2 script significantly affects the overall score. In future assignments, make sure to fully implement the code for calculating SNP enrichments and to include all required outputs, such as the SNP text file and plot. Your understanding of the biological concepts in the README file is on the right track, but could benefit from more detail. Keep working on these aspects to improve your submissions! COME TO OFFICE HOURS IF YOU NEED HELP!