Genome build for dog in RNA STAR

usegalaxy.eu support
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I have noticed that many new reference genomes have appeared in RNA STAR. Would be great if Dog ((UU_Cfam_GSD_1.0/canFam4) Mar.2020) could be added to this collection, then I can complete all my mappings with the same pipeline.

Thanks in advance for your help!

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Hi @Phil

The EU team will be back on their tomorrow, and can comment about what they can do now. ping @wm75 @gallardoalba

The alternative is to get the genome fasta from the UCSC downloads area into Galaxy, then use it as a custom reference genome. The EU server can usually process the largest custom genomes of the three UseGalaxy* servers. But let’s see what they state as the best way to proceed.

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@Phil we would be ok with installing the genome, but are you sure you want canFam4? UCSC lists canFam6 by now, and judging by release date this should be identical to https://www.ncbi.nlm.nih.gov/nuccore/CM000001.4/.

update: yes, checksums between UCSC canFam6 and the nuccore record are identical.

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Hi,

Yes, I think that canFam6 would probably best then. Both seem well enough annotated for RefSeq and UCSC display etc.

Thanks for your help!

Phil

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Hi @Phil,
canFam6 from UCSC is now available for various tools including STAR on usegalaxy.eu.
Please test and let us know if everything works as expected.
Thanks,
Wolfgang

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Hi,

Yes I spotted it was up and working. Seems to work as expected, so thanks again for your help!

Phil

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