Question About Cuffdiff

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Question: Question About Cuffdiff

7.1 years ago by

Alessia D • 30

Alessia D • 30 wrote:

Hi, I am confused about the first line in cuffdiff (using Galaxy on the cloud, not sure if it's different for local instances). It reads: Transcripts:(choose a file)A transcript GTF file produced by cufflinks, cuffcompare, or other source. What file should I load here? I have 4 groups of 2-4 replicates each that I am comparing, and am using the "grouping" option that follows. Should I use one of the files produced by cufflinks? If so, which ones? Or should I rather use the GTF file of RefSeq genes from the UCSC database? Thx!!A

rna-seq cufflinks • 1.0k views

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modified 7.1 years ago by Jennifer Hillman Jackson ♦ 25k • written 7.1 years ago by Alessia D • 30

7.1 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello, The tool documentation provides some help for this: http://cufflinks.cbcb.umd.edu/manual.html#cuffdiff Basically, the ".combined.gtf file produced by Cuffcompare" is the preferred input, but it does depend on how Cuffcompare was run, as explained in the manual. Questions about this tool set can also be sent to the tool authors at: tophat.cufflinks@gmail.com. Best wishes for your project, Jen Galaxy team -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support

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