I was at your USC Galaxy seminar last week, which I found very helpful - thank you!
Glad to hear that you found the workshop helpful. As a reminder, please email questions about using Galaxy and its tools to the galaxy-user mailing list (which I've cc'd). You may get quicker and different responses from community members, and everyone will benefit from the discussion.
I used my recently generated RNAseq data in Galaxy (which was pre-aligned using tophat and already had cufflinks run on it) - I ran cuffcompare with all the gtf files and then cuffdiff for the three pairs (there is 1 control and 3 different drug treatments - no replicates). I got several output files, as expected, but decided just to look at the gene differential expression as a start. Some questions I have are -
1. (very basic question!) which is sample 1 (and corresponding value 1) and sample 2 (and corresponding value 2)in my output file. This is what my output file is called -
90: Cuffdiff on data 37, data 38, and data 60: gene differential expression testing
33,969 lines
Is 37 sample one or sample two? Given the data - I would expect sample 37 to correspond to "value 2" - but I could be wrong. Please let me know!
The best way to figure out which dataset corresponds with Cuffdiff's labels is to click the rerun button in the dataset: sample names correspond directly to the reads datasets (i.e. BAM files) provided as input to Cuffdiff.
2. How do I find the UCSC gene names corresponding with start/end sites - I did input the hg18 UCSC gtf file as a reference