Question: mm10 built-in reference genome unavailable
2
gravatar for yena.oh
19 months ago by
yena.oh70
Canada
yena.oh70 wrote:

Hi,

I'm trying to run cuffdiff with bias correction:

perform bias correction 'yes' -> Reference sequence data 'locally cached' -> Using Reference Genome

I have run cuffdiff previously with this option selected and I was able to select "Mouse(Mus Musculus) mm10." However, now mm10 first shows up for a bit with a spinner circle, then goes to "no options available."

I have seen this github thread about the same error in cuffmerge: https://github.com/galaxyproject/galaxy/issues/388, and it seems like there is no solution yet?

Below shows the parameters from before, when I was able to select the mm10:

Transcripts Cuffmerge on data 262, data 1077, and others: merged transcripts    
Omit Tabular Datasets   False   
Generate SQLite True    

Library normalization method    geometric   
Dispersion estimation method    pooled  
False Discovery Rate    0.05    
Min Alignment Count 10  
Use multi-read correct  True    
Perform Bias Correction Yes 
Reference sequence data cached  
Using reference genome  **mm10**    
Include Read Group Datasets Yes 
Include Count Based output files    Yes 
apply length correction cufflinks effective length correction   
Set Additional Parameters for single end reads? (not recommended for paired-end reads)  No  
Set Advanced Cuffdiff parameters?   No  
Job Resource Parameters no

Now I am unable to select 'mm10' under locally cached sequence data. I'm wondering why what was once available is not anymore.

Any ideas?

Thanks,

Yena

rna-seq cuffdiff • 477 views
ADD COMMENTlink modified 19 months ago by Jennifer Hillman Jackson23k • written 19 months ago by yena.oh70
1

There are some server issues right now. When they clear up I'll see if this can be reproduced now.

The prior issue was resolved by removing a filter that was applied by the tool. The filter would restrict displayed genomes based on the "database" assignment of the inputs. It was resolved but could be back in same format or be related to current server issues.

I am bookmarking this for a reply once sorted out. Thanks for reporting the problem! Jen, Galaxy team

ADD REPLYlink written 19 months ago by Jennifer Hillman Jackson23k
1
gravatar for Jennifer Hillman Jackson
19 months ago by
United States
Jennifer Hillman Jackson23k wrote:

Hello,

The issue should be cleared up now. Please give it a test and let us know if problems persist.

Note: make certain that the input datasets have the metadata "database" assigned before launching the tool form to start the job. To add in the metadata (if needed), click on the pencil icon per dataset to reach the Edit Attributes form - database/build is assigned on the first tab. If changing any attribute, be sure to "save" before leaving the form.

Thanks for reporting the issue, Jen, Galaxy team

ADD COMMENTlink written 19 months ago by Jennifer Hillman Jackson23k
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