Question: ChIP-Seq Histone modification time span study
gravatar for Sudhir Jadhao
5.4 years ago by
Sudhir Jadhao70 wrote:

I am analysing ChIP-seq data for histone protein.

The study is timeline study. It aims to study the binding pattern of histone at different time points(0hr, 2hr, 4hr, 5hr, 6hr). We have two strains namely virulent and avirulent for the time points  (2hr, 4hr, 5hr, 6hr) and 0hr  sample is common.

I hava few questions about analysis listed below:

1) I am doing peak calling with help of MACS2,  What are the parameters to be consider for peak calling ?

2) I dont have Input and mock, should I use one of my sample as control during macs2 peak calling or I do peak calling step without control

3) what should be the minimum number of peaks discover in histone study


chip-seq • 2.0k views
ADD COMMENTlink modified 5.4 years ago by Manvendra Singh2.1k • written 5.4 years ago by Sudhir Jadhao70
gravatar for Manvendra Singh
5.4 years ago by
Manvendra Singh2.1k
Berlin, Germany
Manvendra Singh2.1k wrote:

1.) in -f you specify if your allignment is in bam format or sam format, -g specify the genome which you are mapping (e.g. hs for Human)

-n specify the names of output, -q is FDR threshold, I also give -B , where I also get bedGraph file of peaks, its convinient for some statistical tests. -t is treat, oc is control

-f <SAM/BAM> -g <hs> -n <names> -q <0.05> -B


2. I would suggest you to always call peaks taking Input as control, for Histones and mock as well., Later compare Histones with mock to see the relative enrichment against mock.

3.) It depends, See how many you get first. 

ADD COMMENTlink written 5.4 years ago by Manvendra Singh2.1k

Manu, Thanks for reply

In some research paper suggested that  if  you are studying time span study  then call peak without using control

ADD REPLYlink written 5.4 years ago by Sudhir Jadhao70
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