Question: DESeq - ChIP-seq (including background reads)
0
gravatar for Ian Donaldson
7.7 years ago by
Ian Donaldson70 wrote:
I have previously used DESeq to analyse differential binding in ChIP- seq data (2 replicates of two ChIP samples). I believe the newer versions of DESeq (i have 1.6.1) are able to consider the matching input samples to correct for the background reads. Does anyone have experience of including the background (input) reads in a DESeq analysis? I am afraid i am not sure how to proceed using the vignette. Is there are ChIP-seq workflow anywhere? Thanks! Ian [[alternative HTML version deleted]]
deseq • 526 views
ADD COMMENTlink modified 7.7 years ago by Gordon Brown70 • written 7.7 years ago by Ian Donaldson70
Answer: DESeq - ChIP-seq (including background reads)
0
gravatar for Gordon Brown
7.7 years ago by
Gordon Brown70
Gordon Brown70 wrote:
Hi, Ian, You might consider using DiffBind, which wraps DESeq (and EdgeR) into a set of tools designed for ChIP differential binding. The vignette includes some examples of differential binding analyses. The use of replicates and input or background samples is included. It's part of Bioconductor 2.9, in R 2.14.x. Cheers, - Gord On 2012/01/31 16:46, "Ian Donaldson" <ian.donaldson at="" manchester.ac.uk=""> wrote: > I have previously used DESeq to analyse differential binding in ChIP-seq data > (2 replicates of two ChIP samples). I believe the newer versions of DESeq (i > have 1.6.1) are able to consider the matching input samples to correct for the > background reads. > > Does anyone have experience of including the background (input) reads in a > DESeq analysis? I am afraid i am not sure how to proceed using the vignette. > Is there are ChIP-seq workflow anywhere? > > Thanks! > Ian > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor NOTICE AND DISCLAIMER This e-mail (including any attachments) is intended for ...{{dropped:16}}
ADD COMMENTlink written 7.7 years ago by Gordon Brown70
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 282 users visited in the last hour