I have peak called data of 8 transcription factors (using MACS on BED files).
The format of each file is:
Chr Chr_Start Chr_Stop
Basically three columns.
I want to find the regions where atleast 4 TF bind (Any 4).
Note: I already have a union of these regions in a file and have counted tags for each TF in these region.
The Answer is here: http://biostar.stackexchange.com/questions/13548/bedtools-compare-multiple-bed-files