I am attempting a Hi-C analysis using HOMER. I have generated a tag directory using
makeTagDirectory command as follows.
makeTagDirectory HiC-Unprocessed 3e_HiC_Rep1_1.bam,3e_HiC_Rep1_2.bam -tbp 1
Now I need to filter the TagDirectory for RE site. But my data is 3 enzyme Hi-C. If I provide comma separated list of enzyme sites (see the command below), the output is blank.
makeTagDirectory HiC-processed/ -update -restrictionSite GTAATC,GTATAG,GATTAG -both -genome hg38 -removePEbg
Should I generate separate filtered file for each enzyme? If yes, how should I merge the outputs later?