I'm trying to view the reads that overlap specific regions of a fasta file.
I have a sorted bam file, and I want to use
samtools view -r chr:start-stop to get the reads that overlap that area, but I do not have this organized in terms of chromosomes.
For a while I was using
samtools view -r *:start-stop but the asterisk seems to make it ignore the specified stop/start, and it returns all the reads, instead of just the overlapping ones.
Thank you so much!