HOMER Hi-C with more than one enzyme

Question

[Satyajeet Khare]

Biostars,

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?

Best,

[smurthy]

Hi,

Were you able to figure out an answer for this question, or does someone know how to answer this?

I am trying to process 3 enzyme Hi-C data with HOMER as well and am trying to figure out how I should input the different restriction sites.

Thanks!