Question: Reference genome for RNA STAR
0
gravatar for v.stanulovic
7 months ago by
UK
v.stanulovic0 wrote:

Hi,

I am trying to use STAR for aligning RNASeq data but it doesn't have any reference genome. I would like to use human hg38. Also, would it be possible to add STAR fusion?

Thanks,

Vesna

ADD COMMENTlink modified 7 months ago • written 7 months ago by v.stanulovic0

Hi Jen,

Considering how many post are there about people having problem because of the genome I will wait till the genome indexes are there.

Thanks a lot,

Vesna

ADD REPLYlink written 7 months ago by v.stanulovic0
0
gravatar for Jennifer Hillman Jackson
7 months ago by
United States
Jennifer Hillman Jackson23k wrote:

Hello Vesna,

We are working to add the indexes right now for a subset of databases.

These are the initial genomes that will be added along with status.

You can wait for the deployment to Galaxy Main (http://usegalaxy.org) - OR - if your database is not included in that set of initial genomes and/or you do not wish to wait, a Custom reference genome can be used instead. Please be aware that the tool may fail for exceeding memory resources on larger custom genomes when working at http://usegalaxy.org

I am not sure what the current plans are for adding additional tools from this tool suite. A request ticket has been created for review. Progress can be followed here: https://github.com/galaxyproject/galaxy/issues/4220. Meanwhile, either tool (and all others) are available to install and use in a local or cloud Galaxy sourced from the Tool Shed.

Thanks! Jen, Galaxy team

ADD COMMENTlink modified 7 months ago • written 7 months ago by Jennifer Hillman Jackson23k
1

RNA STAR indexes are ready to use at Galaxy Main (http://usegalaxy.org).

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

Thanks everyone for their patience while we prepared the data and scaled up the memory for the tool!

ADD REPLYlink written 6 months ago by Jennifer Hillman Jackson23k
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