Hello,
Please, would it be possible to add the Arabidopsis thaliana built-in index (TAIR10.1) into the reference genomes for MiRDeep2 Mapper? It is really a key tool in the miRNA field and the Arabidopsis genome is missing, as a model plant species.
Many thanks and best wishes,
Martin Bartas
Welcome @Martin_Bartas
This is a screenshot from UseGalaxy.org. You could work here, too!
Another alternative is to use a Custom Reference genome from the history. This is a link to the same file we have indexed at UseGalaxy.org. Paste the link into the Upload tool at UseGalaxy.eu, use all default settings, and it will load up into your history.
TAIR10 genome fasta
How to select from the history
I put a copy here to make sure it works, so I’ll share it too. You could import and get a copy this way as well.
And .. I’ve also made a request to the UseGalaxy.eu server administrators. This is the tracking ticket to follow → Request: Add TAIR10 to list of genome builds for rbc_mirdeep2_mapper · Issue #1704 · usegalaxy-eu/infrastructure-playbook · GitHub
Hope this gives you some choices and one of these works out for you! Please let us know if it was enough or if you have any questions. 
Dear jennaj,
Many thanks for spending your time on such a comprehensive answer. I am continuing with your suggested Option B (providing a custom genome), as I previously found that transfer between Usegalaxy.eu and Usegalaxy.org can be problematic, due to different chromosome names/nomenclature (e.g. Chr1 vs. chr1 vs. 1). Currently, my jobs are running, we will see…
Once again, thank you for your detailed answer, you are clearly a very enthusiastic person
Best wishes,
Martin
Thanks @Martin_Bartas and totally agree, mixing up genomes at all within an analysis can lead to those mismatched naming (and sometimes length) issues. Using the same custom genome throughout, that you control, is a wise choice.
And thanks for your comments! Reference data questions come up frequently, but yours was novel. It seemed worth listing out all the potential options for whoever may find this next, too!
