how to get the coverage for the entire interval

Question

[alirezamomeni707]

I have aligned my RNA-seq data and trying to get the coverage of 72 nt sequence using bedtools. I also have the coordinate of this sequence. when I get the coverage results, that is only for 62 bases. I want to get the coverage for the entire interval not 5p or 3p. do you know how to solve the problem?

[finswimmer]

Hello,

what was the command you used? And how do you define "coverage"? Total bases sequenced? Average read counts per position? ..?

For bedtools coverage for example there is option -d, which reportes the depth at each position even if it's zero.

fin swimmmer

[alirezamomeni707]

bedtools genomecov -ibam accepted_hits.bam -g GRCh37.p13.genome.fa > output.txt

I want read counts per position.