BINDetect finding only 253 TF binding sites in dataset with ~15,000 peak regions

[mano2991]

TOBIAS BINDetect --motifs Ref/Jaspar/* --signals IC_footprints.bw 7dpi_footprints.bw --genome mm10.fa --peaks all_merged_annotated_IC_TC.bed --peak_header all_merged_annotated_header.txt --outdir foot_printing_manual_pro --cond_names IC 7dpi --cores 30

I'm encountering an issue with TOBIAS BINDetect where I'm getting very few motifs in my regions. The total number of detected motifs is surprisingly low. The maximum TF binding found is only 253 sites, while my input peaks file has ~15,000 sites. I'm not sure what could be causing this large discrepancy.

bindetect_results.txt

[github-actions]

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[hschult]

Hi @mano2991,

indeed the number of TFBS seems low. Maybe your sites are all short so there is not much space for the TFs to bind or there was an issue in one of the preceeding steps (ATACorrect, ScoreBigwig). I recommend you load the files into IGV, I found that this helps a lot to identify problems.