Question: Every time the results of findMotifGenome.pl in HOMER is different
0
gravatar for guandongshang
4 weeks ago by
guandongshang0 wrote:

Hi I am using the findMotifGenome.pl in HOMER 4.10 to find the enriched motif in my bed file. But I found every time I run findMotifGenome.pl, the results is different. I know HOMER will random choose the background peak, so I am wondering whether there is a way to fix the random result.

motif homer • 118 views
ADD COMMENTlink written 4 weeks ago by guandongshang0
1

Hi,

Among the option that the program offers there isn't one to set the seed?

António

ADD REPLYlink written 4 weeks ago by antonioggsousa870

It seems that no seed in HOMER ╮(╯_╰)╭

ADD REPLYlink written 4 weeks ago by guandongshang0
1

according to my esteemed colleague, you can circumvent that issue by providing the same set of custom background sequences via -bg, i.e. -bg <peak/BED file>

ADD REPLYlink written 4 weeks ago by Friederike5.9k

But it seems that it is hard to select bg file when analysing

ADD REPLYlink written 4 weeks ago by guandongshang0

I mean, if you have several peaks to be tesed for enriched motif, you can not set the same bg. you have to choose specific bg file for specific peak?

ADD REPLYlink written 4 weeks ago by guandongshang0

I don't understand the issue with this. I originally thought you were running homer on the same set of peaks and noticed that the results differed. If you supply a different set of peaks every time you run homer why would you NOT expect to see different results? [and if the issue is that you feel it's too much work to generate a custom background peak set for every analysis, well, then I recommend you think about a strategy that can be scripted]

ADD REPLYlink written 29 days ago by Friederike5.9k

Thanks for your reply :) I am sorry I mixed the origin question. Your suggestion is helpful, I am wondering whether you can also give some advice about selecting bg file. Beacuse I noticed the HOMER attempts to select background regions that match the GC-content distribution of the input sequences, but I do not find the relevant specific function in HOMER

ADD REPLYlink written 28 days ago by guandongshang0
1

sorry, can't help with this, but you can check the biostars archive whether anyone has asked that question already (i.e. "How can I mimick the background selection by HOMER?" or the like) and if you don't find what you're looking for, just post it as a new question

ADD REPLYlink written 28 days ago by Friederike5.9k

Thanks again. I will post another question :)

ADD REPLYlink written 27 days ago by guandongshang0
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