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JSuryatenggara / ChIP-AP

An Integrated Analysis Pipeline for Unbiased ChIP seq Analysis
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[ASK] Filtering of Blacklisted Region #10

Closed Shaylee-96 closed 1 year ago

Shaylee-96 commented 1 year ago

Hi, may I know if ChIP-AP filters/removes blacklisted regions before peak calling?

JSuryatenggara commented 1 year ago

Hello Shaylee. Up to the latest version, ChIP-AP does not remove blacklisted regions.

mbassalbioinformatics commented 1 year ago

Hi Shaylee as noted, chipap will not remove blacklisted regions in the current release. This is something we are considering adding in a future release (not for at least another 6-9 months unfortunately).

For now what you can do however is manually exclude blacklisted regions. Following on from a biostar question, you can use the following command.

bedtools intersect -v -abam FILE.BAM -b BLACKLIST.BED > FILTERED.BAM

So what you can do is, generate the scripts for analysis using chipap, but just dont run the analysis. Next, go into the script following alignment and bam generation, write the command to filter out the bam files using the above command and save the script. Then when you run the chipap main script for the whole analysis, it will filter out the bam according to the command and if you write the command correctly, your filtered bam will be passed moving forward into all subsequent peak calling steps. Thus... filtered blacklisted bam files.

Hope that helps.