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Question: HOMER Hi-C with more than one enzyme
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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,

ADD COMMENTlink 2.1 years ago Satyajeet Khare ♦ 1.4k

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