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Handling Dex read density increase in ChIP-Seq data

Hi,

I am looking for a statistical test or model to account for differences in read density increase due to DEX treatment in my replicates in ChIP-Seq (Treatment vs Normal). Can somebody suggest a test that would be suitable to account for this read density increase?

Kind regards

chip-seq statistics ngs
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written by dnamonk • dnamonk

There are plenty, maybe start reading this comparison. Most popular tools are probably DiffBind and csaw.

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written by ATpoint ATpoint

Thanks for the reply but I know it. I don't want to use DeSeq based normalization method. That's why I was thinking if someone can suggest me a statistical test.

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written by dnamonk • dnamonk

Sorry, but I don't understand. The typical workflow is first library normalization and then second a statistical framework to test for differential counts. Asking for a statistical test towards library normalization is kind of intuitive un-intuative. Please elaborate. by the way, csaw offers two different library normalization strategies, well explained in the manual.

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written by ATpoint ATpoint

You are right. What actually I am asking for to rephrase my question is what kind of statistical test they use for interactions part after normalization in DeSeq2 or csaw ? For example between Dex vs untreated

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written by dnamonk • dnamonk

This is all described in the respective manuals and papers, e.g. the manual for csaw here.

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written by ATpoint ATpoint

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