Question: Is it possible to control the coordinate of the peak that HOMER takes into account to annotate?
0
gravatar for nanoide
6 weeks ago by
nanoide30
nanoide30 wrote:

Hi,

So I'm currently annotating some ChIP-sek peaks (coming from macs2 peak calling) using HOMER. I have observed that the "Distance to nearest TSS" column is computed using the center of the peak. My question is, is it possible to change the coordinate of the peak that HOMER uses to give a distance? For example changing it to the beginning of the peak, the end, the summit... I am currently manually correcting this value, but I wondered if this is something HOMER allows.

Any insight would be appreciated, thanks

ADD COMMENTlink modified 6 weeks ago by jared.andrews072.3k • written 6 weeks ago by nanoide30
1
gravatar for jared.andrews07
6 weeks ago by
jared.andrews072.3k
St. Louis, MO
jared.andrews072.3k wrote:

In short, no. That doesn't appear to be an option for HOMER, though making those changes via python/perl/awk after the fact doesn't seem like too difficult a task after the fact, though it is tedious.

ADD COMMENTlink written 6 weeks ago by jared.andrews072.3k
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