# Genome build for dog in RNA STAR

**URL:** <https://help.galaxyproject.org/t/genome-build-for-dog-in-rna-star/9603>\
**Category:** usegalaxy.eu support\
**Tags:** reference-index, custom-genome, reference-genome, custom-build\
**Created:** [March 8, 2023, 2:39pm UTC](https://help.galaxyproject.org/t/genome-build-for-dog-in-rna-star/9603 "2023-03-08T14:39:00Z")\
**Posts on this page:** 6\
**Page:** 1

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**Author:** ![Phil](https://avatars.discourse-cdn.com/v4/letter/p/e95f7d/32.png) [@Phil](https://help.galaxyproject.org/u/Phil)\
**Post date:** [March 8, 2023, 2:39pm UTC](https://help.galaxyproject.org/t/genome-build-for-dog-in-rna-star/9603/1 "2023-03-08T14:39:00Z")

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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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**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\
**Post date:** [March 8, 2023, 9:52pm UTC](https://help.galaxyproject.org/t/genome-build-for-dog-in-rna-star/9603/2 "2023-03-08T21:52:54Z")

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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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**Author:** ![wm75](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/wm75/32/56_2.png) [@wm75](https://help.galaxyproject.org/u/wm75)\
**Post date:** [March 9, 2023, 11:11am UTC](https://help.galaxyproject.org/t/genome-build-for-dog-in-rna-star/9603/3 "2023-03-09T11:11:56Z")

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@Phil we would be ok with installing the genome, but are you sure you want canFam4? [UCSC](https://hgdownload.soe.ucsc.edu/downloads.html#dog) lists canFam6 by now, and judging by release date this should be identical to [https://www.ncbi.nlm.nih.gov/nuccore/CM000001.4/](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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**Author:** ![Phil](https://avatars.discourse-cdn.com/v4/letter/p/e95f7d/32.png) [@Phil](https://help.galaxyproject.org/u/Phil)\
**Post date:** [March 9, 2023, 11:55am UTC](https://help.galaxyproject.org/t/genome-build-for-dog-in-rna-star/9603/4 "2023-03-09T11:55:55Z")

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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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**Author:** ![wm75](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/wm75/32/56_2.png) [@wm75](https://help.galaxyproject.org/u/wm75)\
**Post date:** [March 20, 2023, 10:15am UTC](https://help.galaxyproject.org/t/genome-build-for-dog-in-rna-star/9603/5 "2023-03-20T10:15:42Z")

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

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**Author:** ![Phil](https://avatars.discourse-cdn.com/v4/letter/p/e95f7d/32.png) [@Phil](https://help.galaxyproject.org/u/Phil)\
**Post date:** [March 20, 2023, 10:27am UTC](https://help.galaxyproject.org/t/genome-build-for-dog-in-rna-star/9603/6 "2023-03-20T10:27:44Z")

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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