I am very new to Galaxy. We have performed a comparative analysis between the transcriptomes of different samples. We performed the analysis using Galaxy software (Tophat; CuffDiff; etc). What my PI has done is compiled a list of all the genes differentially expressed between each set, each in a separate excel sheet. So what I have is an excel spreadsheet with a list (usually around 300) of test id, gene id, and locus (ChrX:111111111-22222222222). Initially, we have been identifying each gene individually, one at a time, by pasting the locus into the UCSC browser. This works, but is incredibly tedious. There has to be a better way in Galaxy. I have tried making BED files out of the loci, but so far I have been unable to identify genes using galaxy.
Can someone please explain how I can take my long list of loci and get gene names, ID, function, and possibly some downstream comparative ontologies to begin analyzing.
Like I said, very new to Galaxy and genomics.
Thanks very much