do we need remove PCR duplicate before we look for DE genes
1
0
Entering edit mode
wang peter ★ 2.0k
@wang-peter-4647
Last seen 7.0 years ago
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 -- shan gao Room 231(Dr.Fei lab) Boyce Thompson Institute for Plant Research Cornell University Tower Road, Ithaca, NY 14853-1801 Office phone: 1-607-254-1267(day) Official email:sg839@cornell.edu Facebook:http://www.facebook.com/profile.php?id=100001986532253 [[alternative HTML version deleted]]
• 923 views
ADD COMMENT
0
Entering edit mode
Simon Anders ★ 3.7k
@simon-anders-3855
Last seen 13 months ago
Zentrum für Molekularbiologie, Universi…
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
ADD COMMENT
0
Entering edit mode
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
ADD REPLY
0
Entering edit mode
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
ADD REPLY

Login before adding your answer.

Traffic: 221 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 2.3.6