[BioC] DESeq2 transcript level

[Rao,Xiayu]

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
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www.oeb.harvard.edu/faculty/giribet/

Department of Marine Ecology
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