I would like to use RNA Star (HiSat2 would also be OK) align opposum libraries (monDom5). Both programs indicate that I should contact the Galaxy team if the genome of interest is not available.
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The monDom5 genome is not natively indexed at UseGalaxy.org yet. It doesn’t appear to be indexed at any usegalaxy.* server. We will be added more indexes, including all UCSC genomes, but that is a work in progress. The larger goal is to consolidate all existing indexes across all usegalaxy.* servers, then add more. It will take some time.
Try using a Custom reference genome/build instead. The genome is probably too large for a successful RNA-Star job but maybe not for HISAT2 – so the latter certainly worth a try.
- Preparing and using a Custom Reference Genome or Build
- Mismatched Chromosome identifiers (and how to avoid them)
- Extended Help for Differential Expression Analysis Tools
If the custom genome is too large (jobs fail for resource reasons), then you can consider other options such as setting up your own Galaxy server and natively indexing the genome there.
Ways to use Galaxy: https://galaxyproject.org >> Use
The GVL version of Cloudman is one choice and AWS offers grants. https://aws.amazon.com/grants/
Thanks!
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