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FredHutch / SEACR

SEACR: Sparse Enrichment Analysis for CUT&RUN
GNU General Public License v2.0
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Zero bytes output bed file #75

Open mkim0327 opened 2 years ago

mkim0327 commented 2 years ago

I am using SEACR for CUT&RUN data.

For one of my target + control datasets, I am getting a zero bytes output bed file (norm option). When I run the two files independently (non option), I get bed files with reasonable peaks.

Should I interpret this as that no peaks passed the threshold after normalization?

mpmeers commented 2 years ago

Hi,

Yes, this probably means that the SEACR threshold was set high enough to result in no peaks. You can use a numeric threshold (e.g. 0.01) rather than an IgG control, but keep in mind that there may be false positives included that would otherwise be filtered out.

Mike