MACS2 Output for GREAT
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4.7 years ago
benjyrolls ▴ 70

Hi

I have run the current version of MACS2.1.0 and got these outout 1. treat pile up:bigWig, 2.control Lambda: bedgraph and an 3. peaks:interval file, 4. summits.bed, 5. peaks:narrowPeak and 6. html report.

I will like to find the genes associated with these peaks, but GREAT Stanford only accepts .bed formats my question is which output do i use to find these genes ?

ChIP-Seq MACS2 GREAT • 1.1k views
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4.7 years ago
rbronste ▴ 400

The easiest way is just to pull the data from the narrowPeak files, specifically the peak locations and then add the info required by GREAT, making a new TAB delimited txt file that you can then input into GREAT.

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Am using galaxy is there a way to do this?

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