Hi everyone. I am working on some RNA-seq data. I am interested in finding what are the read counts within an intron for my interest of genes. I have a bam file to start with in which 3rd column of the bam file is basically represented as chromosome1 , chromosome2 and chromosome3. So suppose i have some of my genes of interest on chromosome1 , some on chromosome2 and some on chromosome3, how can I find the number of read counts within the introns of those genes.
Again all i have is a BAM file. Any command line code or anything would be helpful
Thanks in advance