[BioC] DESeq2 transcript level

Thomas Girke thomas.girke at ucr.edu
Fri May 9 19:20:48 CEST 2014


If you assembled your transcriptome, you might be aware that the Trinity site 
has some protocols for this that are based on RSEM and edgeR: 
http://trinityrnaseq.sourceforge.net/analysis/diff_expression_analysis.html
Whether this is the best possible way of addressing this need is a different 
question.

Thomas

On Fri, May 09, 2014 at 04:38:54PM +0000, Alicia R. Pérez-Porro wrote:
> Hi Xiayu,
> 
> I don't think that I can use Cufflink, I don't have a reference genome, I
> created my own reference transcriptome.
> 
> Best,
> Alicia
> 
> 
> 
> --
> Alicia R. Pérez-Porro
> PhD candidate
> 
> Giribet lab
> Department of Organismic and Evolutionary Biology
> MCZ labs
> Harvard University
> 26 Oxford St, Cambridge MA 02138
> phone: +1 617-496-5308
> fax: +1 617-495-5667
> www.oeb.harvard.edu/faculty/giribet/
> 
> Department of Marine Ecology
> Center for Advanced Studies of Blanes (CEAB-CSIC)
> C/Accés Cala St. Francesc 14
> 17300 Blanes, Girona, SPAIN
> phone: +34 972 336 101
> fax: +34 972 337 806
> www.ceab.csic.es
> 
> 
> On Fri, May 9, 2014 at 12:09 PM, Rao,Xiayu <XRao at mdanderson.org> wrote:
> 
> > Hi, Alicia
> >
> > You may try cufflinks. After running cuffdiff, you will get isoform.diff
> > and other files, in which you will find the isoform expression level.
> > Correct me if I am wrong.
> >
> > Thanks,
> > Xiayu
> >
> >
> >
> > -----Original Message-----
> > From: bioconductor-bounces at r-project.org [mailto:
> > bioconductor-bounces at r-project.org] On Behalf Of Alicia R. Pérez-Porro
> > Sent: Thursday, May 08, 2014 6:26 PM
> > To: bioconductor at r-project.org list
> > Subject: [BioC] DESeq2 transcript level
> >
> > Dear Bioconductor users,
> >
> > I am working with differential expression at the transcript (isoform)
> > level. I have 6 different conditions (2 replicates/condition).
> >
> > I want to know if I can use DESeq2 for that or if the package can only be
> > used at the gene level.
> >
> > Thanks,
> > Alicia
> >
> >
> > --
> > Alicia R. Pérez-Porro
> > PhD candidate
> >
> > Giribet lab
> > Department of Organismic and Evolutionary Biology MCZ labs Harvard
> > University
> > 26 Oxford St, Cambridge MA 02138
> > phone: +1 617-496-5308
> > fax: +1 617-495-5667
> > www.oeb.harvard.edu/faculty/giribet/
> >
> > Department of Marine Ecology
> > Center for Advanced Studies of Blanes (CEAB-CSIC) C/Accés Cala St.
> > Francesc 14
> > 17300 Blanes, Girona, SPAIN
> > phone: +34 972 336 101
> > fax: +34 972 337 806
> > www.ceab.csic.es
> >
> >         [[alternative HTML version deleted]]
> >
> >
> 
> 	[[alternative HTML version deleted]]
> 

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