Hello everyone

I am using TOBIAS pipeline (multi step pipeline) for ATAC dataset to identify differential motif across the multiple conditional data. I would like to compare two conditions ( C and T) in order to find the differential motifs.

From manual I found that it takes two input footprints files (output from ScoreBigwig) at BINDetect which is a third step of the pipeline.

TOBIAS BINDetect --motifs test_data/motifs.jaspar --signals test_data/Bcell_footprints.bw test_data/Tcell_footprints.bw

But in my case I have multiple files from each condition (such as 1_T_footprints.bw; 2_T_footprints.bw; 3_T_footprints.bw; 1_C_footprints.bw; 2_C_footprints.bw; 3_C_footprints.bw)

How should I define six footprints.bw files for the differential motif analysis for group C and T at BINDetect step ? If any one has ever used this pipeline, please guide me.

I would really appreciate your help !!