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