I am trying to format the identifiers in my BAM file to match with the GTF file. I used Samtools: IdxStats tool on my BAM file and I got the following output: ibb.co/10rT9tL
I am getting zero counts for RNA seq reads after using featurecount tool in galaxy. I suspect there is some problem with chromosome identifiers in BAM file and GTF file. Can someone guide me in making the identifiers same for both files.