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  • #1

    delete reads that dont overlap with any other reads

    Hi,
    I am a beginner to this area. I have an alignment file in bam/sam format after aligning short reads to my genome of interest using bowtie. I was wondering if there are any tools (or a way by combining tools/steps) to delete non-overlapping reads: reads that dont overlap with any other read in the alignment file.

    Any help will be greatly appreciated.
    Thanks,
    Nitin
    Tags: bowtie, non-overlapping reads, short reads
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