Fwd: Galaxy: RNA-seq analysis problems
Roberta, I'm traveling right now so I'm forwarding your message to our help list. Thanks. ---------- Forwarded message ---------- From: Roberta Galletti <roberta.galletti@ens-lyon.fr> Date: Tue, Sep 11, 2012 at 5:19 AM Subject: Re: Galaxy: RNA-seq analysis problems To: James Taylor <james@jamestaylor.org> 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. On 6/11/2012 5:36 PM, James Taylor wrote: Glad to hear it! Thanks! On Jun 8, 2012, at 9:37 AM, Roberta Galletti wrote: 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: roberta.galletti@ens-lyon.fr e-mail 2: ro.galletti@tiscalinet.it 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.
Hi Roberta, Here is a link to the documentation for replicate handling for the 'NGS: RNA Analysis' tool Cuffdiff: http://cufflinks.cbcb.umd.edu/howitworks.html#reps Other related areas of the documentation are: http://cufflinks.cbcb.umd.edu/faq.html#cuffdiff http://cufflinks.cbcb.umd.edu/howitworks.html#hdif Also see (under 'RNA-seq analysis tools'): http://wiki.g2.bx.psu.edu/Support#Interpreting_scientific_results Good luck with your project! Jen Galaxy team On 9/11/12 7:45 AM, James Taylor wrote:
Roberta, I'm traveling right now so I'm forwarding your message to our help list. Thanks.
---------- Forwarded message ---------- From: Roberta Galletti <roberta.galletti@ens-lyon.fr> Date: Tue, Sep 11, 2012 at 5:19 AM Subject: Re: Galaxy: RNA-seq analysis problems To: James Taylor <james@jamestaylor.org>
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.
On 6/11/2012 5:36 PM, James Taylor wrote:
Glad to hear it! Thanks!
On Jun 8, 2012, at 9:37 AM, Roberta Galletti wrote:
James, I managed to make it work. Thank you for your help. Roberta.
-- Jennifer Jackson http://galaxyproject.org
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