Question: Differential binding ChIP-seq/RNA-seq analysis
0
gravatar for dcheng1
6 months ago by
dcheng10
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 • 357 views
ADD COMMENTlink modified 6 months ago by Gordon Smyth950 • written 6 months ago by dcheng10
1

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 6 months ago by Devon Ryan91k

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 6 months ago by dcheng10
3
gravatar for Gordon Smyth
6 months ago by
Gordon Smyth950
Australia
Gordon Smyth950 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 6 months ago by Gordon Smyth950
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