plotDEXseq rds file not showing up

usegalaxy.org support
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1

Hello,

I am trying to use plotDEXseq, but the rds file generated from my DEXseq job does not automatically populate the input field. If I select it from a browsing menus, “(unavailable)” appears before the file name.

Can someone elaborate on this? Thanks!

Kanishk

2

Hi @Kanishk

Did you assign the database to hg38Patch11? That is not indexed at the public servers but hg38 is. What happens if you change it?

3

Ah, that might be it. I didn’t actually assign a genome when I uploaded the hg38 gtf for DEXseq-Count.

So you’re saying I should re-upload a different version of an hg38 gtf and flatten that genome before finishing DEXseq-Count? Since that’s where hg38Patch11 seems to have been assigned?

Apologies if that’s a naive question!

EDIT: I’ll add that the gtf I used was hg38.p13

4

Hi @Kanishk

Changing the assigned database to be hg38 is likely all that is needed.
https://training.galaxyproject.org/training-material/faqs/galaxy/#changing-database-build-dbkey

  • Galaxy doesn’t assign a database attribute during Upload unless that is specified by the user. The default is no assignment.
  • Galaxy might assign a database attribute for other types of jobs, example = mapping job. The assigned database would be with respect to the genome/build for the reference genome mapped against.
  • Some tool use or require that database attribute to access built-in indexes. If that database assignment isn’t an indexed database, or the assignment is a mismatch for the data content of the file (chromosome names/coordinates differ), expect mismatch errors or odd results.

For the human GRCh38/hg38 genome assembly/build, the version indexed on the public servers is: hg38 and was originally sourced from UCSC.

This can get more complicated (custom genome, custom build, custom database/dbkey). This forum has much help for those topics if needed but might not be needed. Let us know if you need more help.