Tab delineated file containing the number of reads mapping to each gene on chromosome 22. How I can do this with bedtools and shell commands?

Question

[Kevin_Smith]

After an RNA-seq experiment, I got the alignment results in 6 bed format files located in a folder. I'm trying to make a tab delineated file containing the number of reads mapping to each gene on chromosome 22 in each experiment. I will appreciate very much your help. How I can do this with bedtools and shell commands?

Thanks

Answer 1

[Benn]

What you need is the bam files, and a bed file with the coordinates of interest. Then in the unix shell:

bedtools coverage -abam file.bam -b file.bed > results.cov.txt