Question: Fwd: Galaxy: Rna-Seq Analysis Problems
gravatar for James Taylor
6.2 years ago by
James Taylor470
United States
James Taylor470 wrote:
Roberta, I'm traveling right now so I'm forwarding your message to our help list. Thanks. Date: Tue, Sep 11, 2012 at 5:19 AM Subject: Re: Galaxy: RNA-seq analysis problems To: James Taylor <> Hello James, sorry to bother you again, but I've one more question for you. I know that most existing methodologies to analyze RNA-seq data, have a strong dependency on sequencing depth for their differential expression calls and that this results might have a considerable number of false positives. Unfortunately, 1 out of 3 biological replicates of a set of my samples have a much bigger seq depth with respect to the other two samples. Do the programs in the Galaxy NGS: RNA Analysis section take into account this problem and normalize it? Thank you in advance for you help, Roberta Galletti. Glad to hear it! Thanks! James, I managed to make it work. Thank you for your help. Roberta. -- Roberta Galletti, PhD Laboratoire de Reproduction et Développement des Plantes Ecole Normale Supérieure de Lyon, UMR 5667 46, allée d'Italie 69364 LYON cedex 07 FRANCE e-mail 1: e-mail 2: Skype contact: roberta1977 ...A lab is just another place to play.... From 'Dancing naked in the mind field' Kary B. Mullis, Nobel Prize in Chemistry 1993.
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ADD COMMENTlink modified 6.2 years ago by Jennifer Hillman Jackson25k • written 6.2 years ago by James Taylor470
gravatar for Jennifer Hillman Jackson
6.2 years ago by
United States
Jennifer Hillman Jackson25k wrote:
Hi Roberta, Here is a link to the documentation for replicate handling for the 'NGS: RNA Analysis' tool Cuffdiff: Other related areas of the documentation are: Also see (under 'RNA-seq analysis tools'): Good luck with your project! Jen Galaxy team -- Jennifer Jackson
ADD COMMENTlink written 6.2 years ago by Jennifer Hillman Jackson25k
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