I'm not sure if this is something that can be done in galaxy, but if anyone knows how to do it in R that would help aswell.
I've run cuffdiff on my samples and I've selected the output count file function.
When I look at my cuffdiff gene count tracking file, all the rows are under the tracking id (XLOC_00001 etc). Looking at my gene differential expression file though, I can see both the tracking id and the gene name (BRCA1 etc) as I had used a reflat gtf.
I'd like to use the normalised counts file for some other stuff but having the tracking id displayed is not helpful, and changing it manually into the gene names would be too time consuming and daunting. Does anyone know how I can match the tracking id in the one file to the gene name in the other? Either or galaxy or in R?
Any suggestions would be really helpful.