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  • ianh
    Junior Member
    • Nov 2013
    • 1
    #1

    samtools view region not working properly

    Hi all,

    So I have this BAM file of transcriptome mapped to genome. I am trying to extract read numbers of genes with the -c argument on certain regions so like chrx:123456-567890, some worked perfectly fine but some returned the total reads of the whole BAM file. Has anyone encountered similar issues?

    Thanks,

    ian
    Tags: samtools, view
    • dpryan
      Devon Ryan
      • Jul 2011
      • 3478
      #2
      Can you give an example that produces the aberrant behavior? That sounds like a bug.

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