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Bedpe #50

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tan5251 opened this issue Feb 3, 2021 · 1 comment
Open

Bedpe #50

tan5251 opened this issue Feb 3, 2021 · 1 comment

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@tan5251
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tan5251 commented Feb 3, 2021

Hi, for paired-end bam, before i transform the bam files to bedpe, should i remove the unproperly paired reads in the bam files? Because i see only properly paired read were used in BAMPE mode of macs2, i want to know the whether epic2 does this as well.

@endrebak
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As the command line info (under the --guess-bampe flag says):

Only properly paired reads are processed by default (0x1 and 0x2 samtools flags).''

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