Well in that case I will like to use the same gtf file from TAIR 10 that was used by the tophat. But the tophat have the option bult in. How can I point cuffdiff to the same file? Dr. Alejandro Colaneri Departments of Biology University of North Carolina at Chapel Hill 310 Coker Hall, CB# 3280 120 South Road Chapel Hill, NC 27599-3280 Tel: 919-962-2273 fax: 919- 962-1625

From: Jennifer Jackson <jen@bx.psu.edumailto:jen@bx.psu.edu> Date: Thursday, May 30, 2013 8:07 PM To: "Colaneri, Alejandro Cesar" <colaneri@email.unc.edumailto:colaneri@email.unc.edu> Cc: "galaxy-user@bx.psu.edumailto:galaxy-user@bx.psu.edu" <galaxy-user@bx.psu.edumailto:galaxy-user@bx.psu.edu> Subject: Re: [galaxy-user] tophat to cuffdiff without cufflinks

Hello,

You will need to provide a GTF or GFF3 file to Cuffdiff - this is what the tool uses as a reference base to build gene, transcript, and if provided in the annotation attributes, transcript start site and protein groupings to perform the differential analysis.

More details can be found here: http://cufflinks.cbcb.umd.edu/manual.html

Our tutorial and other wiki help is linked from here, see "Tools on the Main Server": http://wiki.galaxyproject.org/Support#Interpreting_scientific_results

Hopefully this helps,

Jen Galaxy team

On 5/30/13 3:15 PM, Colaneri, Alejandro Cesar wrote: Hi

I comparing gen expression data (RNA-seq) in Arabidopsis. Different genotypes, different conditions. Since Arabidopsis is very well annotated I decided to do cuffdiff directly after tophat. However when building my workflow I found that the cuffdiff said a gtf file is necessary. Please see the picture in this email, under INPUT FORMAT. My question is if I can still compare my libraries in the way I designed below. [cid:part1.04070709.03020802@bx.psu.edu] Dr. Alejandro Colaneri Departments of Biology University of North Carolina at Chapel Hill 310 Coker Hall, CB# 3280 120 South Road Chapel Hill, NC 27599-3280 Tel: 919-962-2273 fax: 919- 962-1625

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