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how to get the coverage for the entire interval

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?

alignment rna-seq
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written by alirezamomeni707 • alirezamomeni707

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

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

I want read counts per position.

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written by alirezamomeni707 • alirezamomeni707

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