12 months ago by
For the first part, almost any fasta file can be uploaded and used as a Custom Reference Genome with tools. A Custom Genome can also be of transcript content, the label is general and can apply to both.
Be aware that if the transcript dataset is highly fragmented (sometimes the result from assembly), you might run into memory issues when running jobs at http://usegalaxy.org. Sometimes filtering by length can help (to remove small sequences that didn't fit into the larger assembly, some of which could be contamination of some sort). Still, give it a try first. Jobs that do require more memory (the job will fail with a specific error) could be run on a local/cloud Galaxy with boosted resources allocated.
For the second part, do you mean that you wish to map the NGS reads against the transcriptome? That is certainly possible and a how-to, including a few video examples, are included in the first help link above. If you want to do something else with these data, please reply with more details about what your analysis goals are.
RNA-seq tutorials can be found here. Using your custom genome (aka transcriptome) instead of a pre-indexed genome on the server is definitely possible.
Thanks! Jen, Galaxy team