I have two bed files, a file with peaks, and a file I created to be +/- 1kb of the TSS in mm9.
When I try to use bedtools intersect -v to find all of the peaks that are not overlapping with the 1kb region around a TSS, it returns the same peak file, but with one line different:
$ bedtools intersect -v -a ProE_replicatePeaks.bed -b 1kbTSS.bed > ATAC_Not_Pr.bed
$ wc -l ProE_replicatePeaks.bed
$ wc -l ATAC_Not_Pr.bed
I thought maybe I needed to sort the file containing the region around the TSS, but the same problem occurred.
Any input is appreciated! Thanks.