Question: Performing differential binding analyses between ChIP samples using Deeptools (SES method normalization)
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gravatar for a.rex
20 months ago by
a.rex220
a.rex220 wrote:

I have 2 conditions under which I performed ChIP, each with 3 replicates. I want to perform differential binding analyses between them. I generally get a coverage file using the bamCoverage tool in deep tools (with the SES method) - this allows me to visualise my ChIP signal tracks and compare. But I really want to get a list of regions which are different; in the past peak calling methods have not been useful as the MACS peak calling for my samples tend to be wrong and I think it is because SES is more sensitive at look at enrichment over input.

Any ideas how I can avoid using MACS but still do this DiffBind type of analysis?

chip-seq • 655 views
ADD COMMENTlink modified 11 months ago by Jingyue30 • written 20 months ago by a.rex220
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gravatar for Jingyue
11 months ago by
Jingyue30
United States
Jingyue30 wrote:

You can use Csaw (https://bioconductor.org/packages/release/bioc/vignettes/csaw/inst/doc/csaw.html) it use window-based method for differential binding analysis and can avoid using peaks from MACS2.

ADD COMMENTlink modified 11 months ago • written 11 months ago by Jingyue30
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