Entering edit mode
12.2 years ago
Nicolas Rosewick
11k
Hi,
Very simple question : Is there a tool to count the number of reads that are aligning in an annotated region in the genome. I've a gff file and a bam file (from tophat - paired-end reads 76x2). I thought maybe using bedtools..
Thanks,
N.
If you use the -split argument, it will treat split bam entries as distinct intervals (if that's what you want to do).