3.1 years ago by
The most direct way is to use a GTF reference annotation file that contains the gene_name attribute in the 9th field. There is one for mm10 from iGenomes. Download the tar file locally, unpack it, and then upload the genes.gtf dataset to Galaxy for use with these tools.
Another method is mapping the identifiers contained in the files (supplied by the reference annotation used) to a gene identifier (name or symbol), then linking that in. A common way to do this using a two column file of the mappings along with the "Join, Subtract and Group > Join" tool. UCSC and Biomart will have mm10 annotation mapping transcript identifiers to gene identifiers.
A final method that could be used is examining the overlapping coordinates of transcripts in the result files with a tabular file that contains a gene identifier along with coordinates. This is a less precise method, but is a way to capture some annotation if there are no other options. There are many tools that compare the coordinates of datasets - query by "interval" in the tool search to find the most commonly used.
There are other detailed replies here in Biostar, but it sounds like you have already reviewed those so I won't link them in.
Hopefully this helps! Jen, Galaxy team