Question: Differential binding ChIP-seq/RNA-seq analysis
gravatar for dcheng1
4 weeks ago by
dcheng10 wrote:

Hi! I want to do some cell-type-specific analysis using ChIP-seq. I want to find a list of ChIP-seq peaks locations that are specific to cell types.

I know there are lots of good tools can compare differential binding, such as Diffbind, diffrep, csaw. But it seems those tools can only compare 2 groups.

I'm just wondering if there is a tool that can do differential analysis for more than 3 groups? Any advice would be greatly appreciated!!

sequencing chip-seq • 148 views
ADD COMMENTlink modified 4 weeks ago by Gordon Smyth690 • written 4 weeks ago by dcheng10

Where did you see that CSAW can only do 2 group comparisons? There's no reason that I know of that it should have that restriction.

ADD REPLYlink written 4 weeks ago by Devon Ryan88k

I noticed in the user guide of CSAW, they use two groups, each with 2 replicates. So I assume they can only compare 2. But I not sure about this. Thanks for your clarification! I will try CSAW with 3 groups and see how it works.

ADD REPLYlink written 4 weeks ago by dcheng10
gravatar for Gordon Smyth
4 weeks ago by
Gordon Smyth690
Gordon Smyth690 wrote:

csaw can handle any experimental design that edgeR can, i.e., it can handle any number of groups and any number of explanatory factors.

To quote from the csaw User's Guide (page 41):

A generalized linear model (GLM) will be fitted to the counts for each window using the specified design [22]. This provides a general framework for the analysis of complex experiments with multiple factors. Readers are referred to the user’s guide in edgeR for more details on parametrization.

ADD COMMENTlink written 4 weeks ago by Gordon Smyth690
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