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:FEC3DE9D-5361-483A-BEDD-E7160270E291] 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
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. // //
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