Hi TOBIAS team,
I need some help for running the foot printing. I have 3 conditions, with replicates each. I have merged the bams as suggested per condition and I am trying to run ATACorrect. MY ATAC peaks are called for each replicate with MACs3, then I use IDRpeaks to look for consensus peaks and then I merged the consensus peaks to have a merged bed file with just chr, start and end-
chr1 10001 11396
chr1 13278 13587
chr1 16072 16305
chr1 28778 29824
chr1 79160 79603
chr1 91090 91481
chr1 108780 109381
chr1 180696 181952
chr1 183562 185050
chr1 189436 191885
chr1 199298 200307
Like the above. But then it does not run and tells me that it needs start end peakGroup.

1. My question perhaps has a very obvious answer to it. But should I just add sampleinformation column? But then the common peaks are going to be repeated?
2. Also what if I want to run the fingerprinting for peak overlap groups, such as unique regions, common regions, then can I put them in 1 bed file and run TOBIAS ATACorrect, ScoreBigwig and BINDetect only against those regions?
3. Finally, since I have 3 groups, can I run BINDetect on all 3 of them at the same time or should I run 2 at a time? Also, how do I set a reference level, like condition1: control, condition2:treatment1, condition2:treatment2?
   Thanks in advance.