What is the samtools flag used in bamPEFragment?
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6 weeks ago
Soohyun • 0

I want to know samtools flag used in bamPEFragment.

deeptools • 387 views
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what is bamPEFragment ?

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Select read in bamPEFragment using the conditions below. What is the flag in samtools for the conditions below?

reads = np.array([(abs(r.template_length), r.infer_query_length(always=False))
                          for r in bam.fetch(chrom, start, end)
                          if r.is_proper_pair and r.is_read1 and not r.is_unmapped])
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Flag is probably 66. You can find the SAM/BAM flags by using this helpful page: https://broadinstitute.github.io/picard/explain-flags.html

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