Question: STAR --> option for reference genome
0
gravatar for gupta
7 months ago by
gupta20
gupta20 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 • 423 views
ADD COMMENTlink modified 7 months ago by Jennifer Hillman Jackson23k • written 7 months ago by gupta20
1
gravatar for Jennifer Hillman Jackson
7 months ago by
United States
Jennifer Hillman Jackson23k 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 COMMENTlink written 7 months ago by Jennifer Hillman Jackson23k

Thank you so much Jen. I am using bosTau8.

ADD REPLYlink written 7 months ago by gupta20
1

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

ADD REPLYlink written 7 months ago by Jennifer Hillman Jackson23k

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

ADD REPLYlink written 7 months ago by bazilione0

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 REPLYlink written 7 months ago by Jennifer Hillman Jackson23k
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