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Question: STAR --> option for reference genome
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gravatar for gupta
18 months ago by
gupta • 30
gupta • 30 wrote:

Hi,

I have been trying to test RNA-Star on the Galaxy main server, but in the option for 'Select reference genome', no species appears in the drop-down list. Is this bug only encountered by me or is it a general issue?

I would be thankful for any help and comments.

Best wishes, PG
rna-seq star galaxy • 1.1k views
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modified 18 months ago by Jennifer Hillman Jackson ♦ 25k • written 18 months ago by gupta • 30
1
gravatar for Jennifer Hillman Jackson
18 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

We are working to create built-in indexes right now. We estimate that the first batch will publish in about two weeks. This may or may not contain your target genome. Which are you looking for? We can try to prioritize it in the first batch if it is already a genome natively indexed for other mapping tools (example: Bowtie, HISAT).

For now, using a Custom reference genome is the alternative.

Thanks! Jen, Galaxy team
ADD COMMENT • link written 18 months ago by Jennifer Hillman Jackson ♦ 25k

Thank you so much Jen. I am using bosTau8.

ADD REPLY • link written 18 months ago by gupta • 30
1

Thanks - I'll add that to the short list if possible. It will definitely be included in the full batch.

ADD REPLY • link written 18 months ago by Jennifer Hillman Jackson ♦ 25k

I don't see any Ref genomes. Please add Mus musculus ASAP. Thanks!

ADD REPLY • link written 17 months ago by bazilione • 0

Hello, Index building is in progress. For mouse, mm9 and mm10 are included in the first batch. Thanks! Jen, Galaxy team

https://github.com/galaxyproject/galaxy/issues/1470#issuecomment-307517254

ADD REPLY • link written 17 months ago by Jennifer Hillman Jackson ♦ 25k
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