Hi, I'm a researcher trying to use DESeq2 for analyzing differential loop for fit-hichip results.

I'm curious if I can use it like analyzing differential ChIP-seq using raw contact counts.

I gave a try using DESeq2 for differential loop and the MA plot result was non-symmetric.

Somebody told me it could be the effect of trended biases.

So, I'm trying to correct or remove trended biases in DESeq2.

Is there ways to do it?

Or can't I use DESeq2 for differential loop anlaysis?

If anyone who tried it, please give some advises or directions.

Thank you for your helps.

Woongjae

# include your problematic code here with any corresponding output 
# please also include the results of running the following in an R session 

sessionInfo( )

DESeq2 doesn't have any built in tools for differential loop calling, but I know its been used before as part of differential loop calling packages. I don't remember which packages.

If you don't want to implement the bias correction yourself, I'd just look for packages that wrap this analysis up for you.