Entering edit mode
3.3 years ago
mayalkaul
•
0
Hi,
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!
So it used to work and stopped working just now? Is there a difference in the versions?