gravatar for mayalkaul

2 hours ago by

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!



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