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Help with Samtools flags to get only primary, unique, non duplicate aligned reads
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simulating samtools -f option in pysam
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Question about SAMTOOLS command
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how to extract the sense and antisene bam files from the single end mapping bam file?
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Filtering Pcr Duplicates In Mpileup
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what is bamPEFragment ?
Possibly this command from deepTools: https://deeptools.readthedocs.io/en/develop/content/tools/bamPEFragmentSize.html
Select read in bamPEFragment using the conditions below. What is the flag in samtools for the conditions below?
Flag is probably 66. You can find the SAM/BAM flags by using this helpful page: https://broadinstitute.github.io/picard/explain-flags.html