Inquiry regarding TFBS search space and the use of custom regions

[232322333]

Hi TOBIAS team,

Thank you for developing this powerful tool for ATAC-seq footprinting analysis.I have two specific questions regarding the search space for TFBS (Transcription Factor Binding Sites) and the flexibility of the input regions:

1. Regarding the bound.bed and unbound.bed files —are the TFBS contained in these files across the entire genome or only restricted to the regions in the input peak file?

2. If I do not use ATAC-seq peaks from MACS2 but instead provide a BED file of specific regions of interest (such as a curated list of enhancers, promoters, or specific regulatory elements), is this a valid approach?

Thank you for your time and for this excellent tool!

[hschult]

Hi,

1. The peaks are expected to be the combination of all open chromatin regions across the conditions. So it is restricted to the input peaks unless further restricted with the --output-peaks parameter.
2. If you want to only look at certain open chromatin regions of interest, I suggest using the --output-peaks parameter. Otherwise, you may create bias or normalization issues when using only part of the open chromatin.

I hope that helps

Cheers
Hendrik

[232322333]

Hi Hendrik,

Thank you for the clarification and helpful explanation.

I have a quick follow-up question regarding the --output-peaks parameter. I checked the wiki and the supplementary materials of the paper but could not find any description of this option. Could you please point me to where this parameter is documented, or briefly explain how it is intended to be used?

Best regards,
Fei

[hschult]

Try the help message of the respective tool. In this case, TOBIAS BINDetect --help

[232322333]

Thank you for the helpful tip! I'll check the help message of the respective tool.