using samtools view without a chromosome

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!

samtools reads alignment

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written 5.6 years ago by mayalkaul •

So it used to work and stopped working just now? Is there a difference in the versions?

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written 5.6 years ago by Ram

0 answers

No answers yet.

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