Question: chipseq data normalization
3
gravatar for kanwarjag
5.6 years ago by
kanwarjag1.0k
United States
kanwarjag1.0k wrote:

I have 4 chipseq data (Bam files) files from Input, control treated and knockout of a gene. Now while preparing these samples different amount of DNA was processed/ pooled, because of inherent experimental problems. I want to normalize all four samples to fixed value  and then analyze these samples. How best/ tool/ software I can do this normalization? Is it possible to get bam/ sam files of such normalized data as I would like to use NGS plot to generate figures for binding pattern.

 

Thanks

 

 

normalization chipseq • 3.0k views
ADD COMMENTlink modified 5.6 years ago by Ying W4.0k • written 5.6 years ago by kanwarjag1.0k
2
gravatar for A. Domingues
5.6 years ago by
A. Domingues2.2k
Dresden, Germany
A. Domingues2.2k wrote:

I am using deepTools for my ChIP (and RNA-seq) normalizations and plotting:

https://github.com/fidelram/deepTools/wiki/Normalizations

For instance you can normalize to sequencing depth and input. The output, however is bigwig, but since this format is integrate in the other deeptools, it is ok for most purposes.

ADD COMMENTlink written 5.6 years ago by A. Domingues2.2k
2
gravatar for Ying W
5.6 years ago by
Ying W4.0k
South San Francisco, CA
Ying W4.0k wrote:

Look into using DBChIP which can normalize based on non-peak regions or DiffBind which can normalize based on effective or full library size. The DBChIP paper is a good start if you are unsure what these normalization methods are.

ADD COMMENTlink modified 5.6 years ago • written 5.6 years ago by Ying W4.0k
0
gravatar for Ming Tang
5.6 years ago by
Ming Tang2.5k
Houston/MD Anderson Cancer Center
Ming Tang2.5k wrote:

you can normalize to the library size.

ADD COMMENTlink written 5.6 years ago by Ming Tang2.5k

Could you please explain a little more on how we normalize to library size. Is there a package/ tool?

ADD REPLYlink modified 9 days ago by RamRS25k • written 5.6 years ago by kanwarjag1.0k
1

deeptools will do that for you: https://github.com/fidelram/deepTools/wiki/Normalizations#bamCoverage

ADD REPLYlink written 5.6 years ago by A. Domingues2.2k
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