Question: Using HOMER called peaks in DiffBind
0
gravatar for Hesh
2.0 years ago by
Hesh0
University of Washington
Hesh0 wrote:

Hi, 

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

 

Thank you

 

diffbind homer • 609 views
ADD COMMENTlink modified 2.0 years ago • written 2.0 years ago by Hesh0
Answer: Using HOMER called peaks in DiffBind
0
gravatar for Rory Stark
2.0 years ago by
Rory Stark3.0k
CRUK, Cambridge, UK
Rory Stark3.0k wrote:

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 COMMENTlink modified 2.0 years ago • written 2.0 years ago by Rory Stark3.0k

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 REPLYlink written 2.0 years ago by Gord Brown590
Answer: Using HOMER called peaks in DiffBind
0
gravatar for Hesh
2.0 years ago by
Hesh0
University of Washington
Hesh0 wrote:

Thanks a lot!

ADD COMMENTlink written 2.0 years ago by Hesh0
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