Question: Peak calling macs vs Homer
gravatar for saurabh.j.pradhan
9 days ago by
saurabh.j.pradhan0 wrote:

Hi, I am trying to analyze ChIP seq data for a factor which do not behave as a typical transcription factor. When I am using MACS2 i hardly get any significant peaks. Around 20. And when I perform Homer I get 20000. I am not able to understand which peak caller to go for. Macs is not even picking up peaks which I can visually see in IGV. Can somebody help me to understand the reason behind it. I am using broad peak calling option. If I decide to go ahead with Homer then on what basis I should filter my peaks. I am planning correlated binding profile with transcriptome data further.

chip-seq • 151 views
ADD COMMENTlink written 9 days ago by saurabh.j.pradhan0

Can you post the Macs2 and homer commands ?

ADD REPLYlink written 9 days ago by geek_y7.8k

agreed. you should at least post the commands to show what you have tried.

ADD REPLYlink written 8 days ago by tangming20052.1k

Why would you use broad peak option if you are calling a TF?

ADD REPLYlink written 7 days ago by aka001130
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