[BioC] do we need remove PCR duplicate before we look for DE genes

[Lucia]

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
> 
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