3 months ago by
The custom genome/annotation data is too large to process with the RNA STAR mapper at Galaxy Main https://usegalaxy.org even with the input corrections. This results in an empty BAM output that cannot be indexed, triggering the metadata problems.
This means that you'll need to do one of these:
- use HISAT2 instead
- run the RNA STAR job using an indexed built-in genome at Galaxy Main (along with a reference annotation dataset that is a match: eg: same genome build/common chromosome identifiers).
- consider starting up your own Galaxy server and provide it with enough memory to run.
For items 2 & 3, please be aware that it is possible that the job may still remain too large to execute, even when using a built-in genome or given more resources at your own Galaxy server. RNA STAR uses much more memory during job execution than the other mapping tools - whether used in Galaxy or not.
I tested HISAT2 with your data and the job completed successfully. What I did:
- corrected the custom genome format
- removed the database assignment from the fastq inputs
- changed the datatype for the fastq inputs to
- no reference annotation was used (HISAT2 accepts
gtf formatted annotation, not
How to do the above and where to obtain reference annotation in
gtf format is covered in the FAQs I linked in the original comment.
Galaxy tutorials for RNA-seq with workflow/tool example usage: https://galaxyproject.org/learn/
Thanks! Jen, Galaxy team