Coverage per gene

Question

[gubrins]

Hey,

I'm working with bedtools trying to find out the coverage of several target regions. I have my bam files and my target regions in a .bed file and I'm running this:

bedtools bamtobed -i WA01.bam | bedtools coverage -a - -b mit.bed > exons.mit.coverage

When I open the exons.mit.coverage file, in the coverage section I just have 0s in the areas that are not matching my target genes and 1s in the areas of my target genes, as I have coverage per read.

My question: How can I obtain coverage per gene and not coverage per read?

I imagine I can filter this out, selecting the reads with a good quality score per gene, but I think this should be already implemented anywhere else that I don't know

Thanks for your help! :)

[Pierre Lindenbaum]

see How to calculate average coverage for all genes

[gubrins]

I'm also going to check that link, thanks!

Answer 1

[ATpoint]

Switch -a and -b.

bedtools bamtobed -i WA01.bam | bedtools coverage -b - -a mit.bed > exons.mit.coverage

[gubrins]

Thank you very much!!! It worked!! Now I need to filter the reads per quality, because I had all of them together.

[gubrins]

I was trying to send you a private message @ATpoint but I don't know if it's possible to send them. Thanks for the help, I've seen that you have been replying to some of my messages lately and the help is really apreciated!

[GenoMax]

It is not possible to send private messages to Biostars users via this site.