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  • #1

    How to set a flag is mapped in sam/bam?

    In sam/bam, there is flag which indicate this read is mapped/unmapped. I am wonder when this flag is set to mapped/unmapped? What is the criteria? If used different mapping tools, eg, bowtie, bwa, eland. Do they use the same criteria?
    Thank you
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  • #2
    No, they are different algorithms so will map different reads.

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