I am using galaxy to analyze some RNASeq data. I have a couple of questions with regards to it: 1. When we are uploading data, one of the fields to be populated is "Genome". Why or where is galaxy using the genome information during file upload? 2. During Cuffcompare analysis, we can provide 3 files, two GTF files output from cufflinks and a reference annotation file. When cuffcompare how does it use the annotation file? 3. If cuffcompare is run using one cufflink GTF file and one reference annotation file, what are we supposed to do during cuffdiff analysis where you have to provide 2 sam/bam files?

Is there any documentation/manual (except for what is on the UI) around that can help answers these (and some other basic questions I have).

Thanks a lot for your help.
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