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@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@r-project.org [mailto:
> bioconductor-bounces@r-project.org] On Behalf Of Alicia R. Pérez-Porro
> Sent: Thursday, May 08, 2014 6:26 PM
> To: bioconductor@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. PÃ©rez-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/AccÃ©s 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]]

