I have used Galaxy to do RNASeq analysis. I don't quite understand the Cuffcompare part.
When running cuffcompare (considering that I am using Cuffdiff afterwards), do I have to provide the 2 assembled transcript files (for the 2 samples on which I want to later run cuffdiff) and a reference file? The reason I am not sure is because when I run cuffdiff, I have to provide the gtf output of cuffcompare and the 2 bam files that I want to run cuffdiff on. I have tried to readup in the galaxy manual without much luck.
Thanks for your help!
When running cuffcompare (considering that I am using Cuffdiff afterwards), do I have to provide the 2 assembled transcript files (for the 2 samples on which I want to later run cuffdiff) and a reference file? The reason I am not sure is because when I run cuffdiff, I have to provide the gtf output of cuffcompare and the 2 bam files that I want to run cuffdiff on. I have tried to readup in the galaxy manual without much luck.
Thanks for your help!
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