I've recently processed a number of ATACseq samples using the ENCODE workflow, but did not keep any of the _summit.bed files by MACS2.
I believe I still have this information in my IDR narrowPeak files under the Point-source column (chr start + point source value) and can use this information to recapitulate the summit positions so I can generate fixed length peaks for eventual motif analysis.
My understanding is through the point-source column, the BED6+4 format narrowPeak format contains the same summit information (also output by MACS2 as _summit.bed) or the location in the peak with the highest fragment pileup?
I apologize if this is obvious, I only recently adopted this ENCODE based workflow (used to keep the summit files...) and wanted to triple check this before I embarked on a lot of work. I haven't ever made use of the point-source data in peak files and want to make sure I'm not missing something.
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Ready2Rapture •
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I am also new to ENCODE atac pipeline. However, I believe the 10th column in the narrowPeak file provides the number of bp away from the chromosome start position (2nd column) that the summit sits. So summit would be $2+$10.
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