[WIP] ATAC-Seq workflow #26
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Co-authored-by: Clay McLeod <[email protected]>
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@claymcleod - In response to your comment (#24 (comment)). I think an open question is what is our goal for St. Jude Cloud? For analysis, ATAC-Seq typically has duplicate reads removed, low mapping quality (MAPQ < 30) removed, chrM-aligned reads removed, duplicate reads removed, and reads overlapping ENCODE sites removed. In this proposal, I've opted to unmap those reads rather than remove them. This leaves the BAM in a state much closer to analysis-ready. Otherwise, we could skip those steps and leave them to the user/consumer as it isn't overly difficult to remove those reads. Do we want to produce analysis-ready files or should we opt for a simpler minimal approach? |
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Continuation of #24