how to determine number of subreads that spanned across certain region

Question

[wes]

May I know how to determine the number of subreads that span a certain region besides counting the subreads manually using the IGV?

Answer 1

[Alex Reynolds]

Here's one way to do a count on an ad-hoc region (replace values Z, A, and B, as desired):

$ bedmap --echo --count --delim '\t' <(echo -e "chrZ\tA\tB") <(bam2bed --reduced < reads.bam)

If you have a file of regions:

$ bedmap --echo --count --delim '\t' <(sort-bed regions.bed) <(bam2bed --reduced < reads.bam)