Error when running DESeq2 in Galaxy · Biostar

This is a test version of Biostars. For the public version, visit https://www.biostars.org.

Error when running DESeq2 in Galaxy

I am trying to perform differential expression on RNASeq from NASA's Genelab data repository. I used STAR for genome alignment and FeatureCounts to generate count files in the tabular format.

However, when importing the feature counts output to the DESeq2 tool with two different factor levels, I repeatedly get the following error: cannot create 'R_TempDir'. It might be the lack of permissions on the Galaxy server to create the temporary directory.

Has anyone ever encountered this error on the platform before? Any idea for a possible solution would be greatly appreciated.

enter image description here

galaxy deseq differential rna-seq

• 1,410 views • link

written 6.1 years ago by noran •

1 answer

Please post this over at Galaxy help forum for immediate help: https://help.galaxyproject.org/

If you are running this on a local Galaxy mirror then you may want to contact your local galaxy admins.

• 0 views • link

written 6.1 years ago by GenoMax

Log in to answer this question.

More posts like this

Sanity Check on RNA-Seq featureCounts / DESeq2
written 7.3 years ago by gwebste7 •

Hello. My colleague and I are trying to run a differential gene analysis to compare protein activity in cutthroat trout under normal and heat stressed …
Tutorial: Getting the lineage of an organism from NCBI taxonomy data
written 8.0 years ago by vimalkvn

This is a method I followed to get an organism's complete lineage from [NCBI][1] taxonomy data. The procedure involves: 1. Creating a MySQL database. 2. …
Forum: Erik Garrison of FreeBayes uses this
written 11.7 years ago by Istvan Albert

[Erik Garrison][1] received his Bachelors degree in 2006 majoring in Social Studies at Harvard University. He then went on to work as a Software Engineer …