Zero bytes output bed file

[mkim0327]

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]

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