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Question: Reference transcriptomes for kallisto in Galaxy
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gravatar for Ray_Enke
4 months ago by
Ray_Enke • 0
USA/Harrisonburg, VA/James Madison University
Ray_Enke • 0 wrote:

Hello,

I'm interested in using the Kallisto quant and psudo tools in Galaxy to analyze human, mouse, and chicken RNA-seq data sets. There are however, no reference transcriptomes to choose from at the moment. Is there an ETA on having some stock built in refs to choose from? I'm most interested in human hg38, mouse mm10, and chicken galGal5.

Thanks!
kallisto galaxy rna-seq • 246 views
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modified 4 months ago by Jennifer Hillman Jackson ♦ 25k • written 4 months ago by Ray_Enke • 0
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gravatar for Jennifer Hillman Jackson
4 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

As far as I know, there are no current plans to natively index transcriptomes for these tools. Instead, upload your own and use it from the history.

Related tickets for this tool: https://github.com/search?q=org%3Agalaxyproject+Kallisto&type=Issues

You could make a request to have this data added (if possible) at the IUC tool developer's repository. Additions are unlikely to be immediate, as there are some data federation tasks in progress across the usegalaxy* servers that need to be sorted out first.

Thanks! Jen, Galaxy team
ADD COMMENT • link modified 4 months ago • written 4 months ago by Jennifer Hillman Jackson ♦ 25k
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