Question: Question About Cuffdiff
0
gravatar for Alessia D
6.8 years ago by
Alessia D30
Alessia D30 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 • 907 views
ADD COMMENTlink modified 6.8 years ago by Jennifer Hillman Jackson25k • written 6.8 years ago by Alessia D30
0
gravatar for Jennifer Hillman Jackson
6.8 years ago by
United States
Jennifer Hillman Jackson25k 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
ADD COMMENTlink written 6.8 years ago by Jennifer Hillman Jackson25k
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