13 months ago by
1 - Use a reference annotation dataset in the analysis that includes the target gene names as an attribute. This is "gene_name" if using Cuffdiff and a GTF file; some other tools require gene_id (GTF) or Gene (if in GFF3 format). iGenomes is a good source if your genome/version is included (down the tar file locally, unpack it, then just upload the genes.gtf dataset to Galaxy).
2 - Find a file that maps the two IDs and use the tool Join two Datasets side by side on a specified field. The UCSC tables named like "xref" are one choice (if your genome is supported there): http://genome.ucsc.edu
3 - This will not work for your case, but for others wanting to map IDs, the tool UniProt ID mapping and retrieval is often helpful.
Hope that helps! Jen, Galaxy team