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Question: HISAT2 - no reference genome available
1
gravatar for delorez
2.8 years ago by
delorez • 10
delorez • 10 wrote:

HISAT2 does not have any options for a built-in reference genome.

I need mm10.

Source for the reference genome to align against

I selected:

Use a built-in genome

The next line:

Select a reference genome

The pull down menu says:

No options available

And underneath says 'If your genome of interest is not listed, contact the Galaxy team'

Did I do something wrong? Please advise.

Thanks!

 

 
rna-seq alignment • 1.7k views
ADD COMMENT • link •
modified 2.8 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.8 years ago by delorez • 10
3
gravatar for Jennifer Hillman Jackson
2.8 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

This tool is new and index creation is in progress. Use our test server for now to try out the the latest (mm10 is included, for all tools). These will all be promoted to http://usegalaxy.org near-term (but no promised release date yet!).

For details about genome indexes in progress, the test server link, and how to request genome additions plus send in feedback from using indexes on the test server, please see this Github ticket: https://github.com/galaxyproject/galaxy/issues/1470

Meanwhile, at http://usegalaxy.org, using a Custom Reference genome is the right way to use mm10 with this tool: https://wiki.galaxyproject.org/Support#Custom_reference_genome

Thanks, Jen, Galaxy team

 
ADD COMMENT • link modified 2.8 years ago • written 2.8 years ago by Jennifer Hillman Jackson ♦ 25k

Update: mm10 and many other genomes were made available to this tool several months ago. Thanks!

ADD REPLY • link written 22 months ago by Jennifer Hillman Jackson ♦ 25k
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