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From: Ogan <ab...@gm...> - 2014-05-09 18:43:03
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Dear all, I have run into something unexpected and maybe someone already knows the answer. I am counting duplicate reads in bam files using 'samtools view -cf 1024 sample.bam' vs counting lines with 'd' in flag string in 'samtools view -X sample.bam' . In the latter case I am getting 1034 less reads out of 699K duplicate reads. I would have assumed that the numbers would be the same. Is this expected or am I missing something? Thank you all, Ogan |