Day 2 Answer Key

Handling peak files using bedtools

1. Use the wc -l command to check how many peaks were filtered due to an overlap with blacklisted regions. Report the number of peaks before and after the filtering for each WT sample.

Answer: For wt_sample1, the number of peaks before and after filtering is 14,294 and 14,134, respectively. For wt_sample2, the number of peaks before and after filtering is 20,013 and 19,829, respectively.