User: armandorp

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armandorp60
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Posts by armandorp

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Comment: C: Remove reads counts overlapping with blacklist regions in BAM files
... Thanks Devon. Do you mean to use deeptools before calling peaks to get a kind of marked BAM file for these regions? So you don´t recommend to remove blacklisted regions in the alignments, but the reads/ high-signal associated with blacklisted regions can affect the peak calling with MACS2. ...
written 3.7 years ago by armandorp60
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Remove reads counts overlapping with blacklist regions in BAM files
... Hi all, I am preprocessing some bam files for differential binding analysis. I have read that some people recommend removing blacklist regions (human) before to do the peak calling. Do you have any suggestions how directly extract the read counts in these regions using maybe samtools? Thanks, Ar ...
chip-seq samtools written 3.7 years ago by armandorp60 • updated 19 months ago by Biostar ♦♦ 20

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Appreciated 8 months ago, created a post with more than 5 votes. For Remove reads counts overlapping with blacklist regions in BAM files
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