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Question: Do I need to normalize the ChIP-seq BAM files before run MACS?
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gravatar for Gene Genome
4.3 years ago by
Gene Genome • 20
United States
Gene Genome • 20 wrote:

Hi Everyone,

The experimental ChIP-seq datasets I am analysing have two times of aligned reads than control datasets. Do I need to normalize the datasets based on read number (depth) before run MACS?

Thanks.

Jianguang
chip-seq • 3.8k views
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modified 4.3 years ago by Bjoern Gruening ♦ 5.1k • written 4.3 years ago by Gene Genome • 20
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gravatar for Bjoern Gruening
4.3 years ago by
Bjoern Gruening ♦ 5.1k
Germany
Bjoern Gruening ♦ 5.1k wrote:

Hi Jianguang,

yes normalizing your data for various biases are recommended. Have a look at the deepTools wiki page. The documentation is quite good and we are using these tools a lot in our lab.

Cheers,

Bjoern
ADD COMMENT • link written 4.3 years ago by Bjoern Gruening ♦ 5.1k
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