Question: RNA STAR -Gapped-read mapper for RNA-seq data (Galaxy Version 2.5.2b-0)
1
gravatar for utkarsh.kapoor
16 months ago by
University of Vienna, Austria
utkarsh.kapoor50 wrote:

Hi,

Now that Galaxy has introduced RNA Star in their list of tools in NGS: RNA Analysis, I wanted to try it out. However, when I want to select the reference genome from its drop down menu, there are no options whatsoever. I want to use Mouse (mm10) for my analysis but I don't see any genome in the list. Is this a plugin or version issue?

Since I read "If your genome of interest is not listed, contact the Galaxy team" right next to this menu option, I ask your help for the same.

Thanks a lot,

Utkarsh

rna-seq star • 1.1k views
ADD COMMENTlink modified 16 months ago by Jennifer Hillman Jackson25k • written 16 months ago by utkarsh.kapoor50
0
gravatar for Jennifer Hillman Jackson
16 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

We will be adding STAR indexes very soon. The genome mm10 will be included.

Meanwhile, a custom reference genome can be used. This is how: https://galaxyproject.org/learn/custom-genomes/

Thanks! Jen, Galaxy team

ADD COMMENTlink modified 16 months ago • written 16 months ago by Jennifer Hillman Jackson25k

Hi Jennifer,

Thanks a lot for the response. Just to get an idea, please define "soon" :) Are you talking a couple of days or weeks?

Best,

Utkarsh

ADD REPLYlink written 16 months ago by utkarsh.kapoor50

We hope to get this out today, but it may be later in the week.

The indexes are available right now on the Test server: https://test.galaxyproject.org

Small warning: The tool may fail for exceeding compute resources on the Test server right now. This will result in certain job failing for a memory error. We are working to fix that by allocating more resources. User quota is much smaller on the Test server and other tools may or may not work, as we really do test here. I suggest waiting until the full deployment at Galaxy Main is ready before running any serious analysis, but you and others are welcome to test the current RNASTAR indexes and report any problems with that specific tool (except for the exceeding memory issue as it is a known).

ADD REPLYlink written 16 months ago by Jennifer Hillman Jackson25k

Hi Jennifer,

I tried to look this up again this morning and I could'nt find the indexes for STAR or even Salmon in there. Is this an issue on my end or have the indexes not been added yet? I am referring to the Galaxy Main Server and not the Test Server.

Best,

Utkarsh

ADD REPLYlink written 11 months ago by utkarsh.kapoor50

Hi - The index for mm10 and others are there. Please see: https://imgur.com/a/KL0Jr

ADD REPLYlink modified 11 months ago • written 11 months ago by Jennifer Hillman Jackson25k

Thanks. I found the information for STAR. Could you please share the info for Salmon too? Currently, I see "No Options Available"

ADD REPLYlink modified 11 months ago • written 11 months ago by utkarsh.kapoor50

There are no transcriptomes natively indexed for Salmon at https://usegalaxy.org. This is on purpose since targets can vary and update quite frequently. So use the option "Select a reference transcriptome: Use one from your history".

Locate your transcriptome of interest and load it into Galaxy in fasta format into your history. Then any datasets with the fasta datatype in your history will appear in the drop-down menu. Use FTP to upload you have the data locally and it is over 2 GB. Or a public URL link. Or a Get Data tool can be used to transfer directly from the data provider to Galaxy in many cases.

Example: for mm10 known transcriptomes, UCSC can be a good source if you plan to use the data with the mm10 genome in a downstream step. Review the tracks in Genes and Gene Predictions with the Get Data > UCSC Main data retrieval tool. RefSeq Genes is one option but there are others.

More about using Salmon: https://galaxyproject.org/tutorials/rb_rnaseq/

ADD REPLYlink modified 11 months ago • written 11 months ago by Jennifer Hillman Jackson25k
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