Question

Using HOMER called peaks in DiffBind

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Hesh ▴ 10

@hesh-14437

Last seen 4.1 years ago

University of Washington

Hi,

Can I use HOMER called peaks in DiffBind without making any changes to the peaks file (HOMER output file)?

Thank you

diffbind HOMER • 2.6k views

ADD COMMENT • link 7.1 years ago • updated 7.0 years ago Hesh ▴ 10

score 0 · Answer 1 · 2017-12-08

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Rory Stark ★ 5.2k

@rory-stark-5741

Last seen 8 weeks ago

Cambridge, UK

You can use the pos2bed.pl utility that comes with HOMER. There is a discussion of this here:

DiffBind: reading in peaksets generated by Homer2

See particularly Gord's answer near the top.

Cheers-

Rory

P.S. We still have an "add support for HOMER peak format" feature in our list of to-do, maybe someday soon?

ADD COMMENT • link 7.1 years ago Rory Stark ★ 5.2k

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Note also that in "factor" mode, HOMER produces fixed-width peaks. For very strong peaks, that may mean that most of the reads are outside the range of the called peak (e.g. it gives you 200bp wide peaks, but the bulk of reads in a very strong peak might be more than 100bp from the centre). If you're looking at differential binding, this can give misleading results, since reads that are off the edge of the called peaks won't be counted.

ADD REPLY • link 7.1 years ago Gord Brown ▴ 670

score 0 · Answer 2 · 2017-12-10

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Hesh ▴ 10

@hesh-14437

Last seen 4.1 years ago

University of Washington

Thanks a lot!

ADD COMMENT • link 7.0 years ago Hesh ▴ 10