Hi everybody, I have bam files for RNAseq, and I know the coordinates for specific exons of interest. I would like to know if there is any way to overlap my bam files over those specific coordinates and get the coverage for those regions. I usually use bedtools coverage, but to compare between samples. I was wondering if I can create a bed files with my coordinates and do:
bedtools coverage -a my.bam -b mycoordintes.bed -s
will that work?