Hi Lucia, I'm not Simon, but my preferred strategy regarding duplicate removal for TF ChIP-seq is to remove duplicates when peak-calling, but not when doing read-based analysis (i.e. using a differential count algorithm on small, defined genomic bins) for similar reasons to the ones Simon described in his response; though I find my dynamic range is more like 1:1,000 than 1:100,000, and that's on a really good day. See the "Effect of redundant reads on narrow peak calling" section of "Systematic evaluation of factors influencing ChIP-seq fidelity" for a brief discussion on this topic. http://www.nature.com/doifinder/10.1038/nmeth.1985 Jonathan ________________________________________ From: bioconductor-bounces@r-project.org [bioconductor- bounces@r-project.org] on behalf of Lucia [luciap@iscb.org] Sent: 13 June 2013 19:20 To: Simon Anders Cc: bioconductor at r-project.org Subject: Re: [BioC] do we need remove PCR duplicate before we look for DE genes Hi Simon, I wonder what your take is on ChIPseq experiments and duplicate removal I tend to cover about 10% of the genome with both RNAseq and different types of ChIPseq, but I am not sure what the dynamic range is for the second and what the effect will be Thanks Lucia Sent from my iPhone On Jun 13, 2013, at 1:09 PM, Simon Anders <anders at="" embl.de=""> wrote: > On 13/06/13 17:06, Wang Peter wrote: >> in RNA-seq data analysis, >> do we need remove PCR duplicate before we look for DE (differential >> expressed)genes >> some people say yes, some say no > > Here's my reply from last time this was asked on this list: > > https://stat.ethz.ch/pipermail/bioconductor/2011-February/037810.html > > _______________________________________________ > 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 _______________________________________________ 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