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loosolab / TOBIAS

Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal
MIT License
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Peak within footprint region #157

Closed loganminhdang closed 1 year ago

loganminhdang commented 2 years ago

Hi, this is probably a simple question, but can footprint regions still have peaks? I'm talking about a case such as this:

image

I wouldn't expect footprints to have this trace (normally, we see a dip indicating transcription factor binding and don't observe such a sharp peak). I wonder if you know what this peak may mean?

msbentsen commented 2 years ago

Hi,

Yes, a footprint might still have peaks in the middle. I have seen this quite a lot, and I don't know how to explain it biologically, but it might be some Tn5 bias leftover which was not able to be corrected. Could also be a true biological signature of whatever TF is binding there, which is not fully understood yet. In such cases, I would still say that SCNSD has a stronger footprint than SCNCT due to the total height of the signal.

For the error message, can you create a second issue for that? It helps me keep the issues separated. Thank you!