differential loop using DESeq2
0
Entering edit mode
woongjaej • 0
@woongjaej-13388
Last seen 4 weeks ago
Korea/Seoul/Yonsei University, College …

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( )
hichip DESeq2 fithichip differentialloop • 113 views
ADD COMMENTlink
0
Entering edit mode

Cross-posted here: https://www.biostars.org/p/486360/ (includes the MA-plot)

ADD REPLYlink
0
Entering edit mode
@mikelove
Last seen just now
United States

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.

ADD COMMENTlink

Login before adding your answer.

Similar Posts
Loading Similar Posts
Traffic: 222 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.4