Hello, I am trying to run featureCounts on my BAM file using a built-in genome from Galaxy. I wrote "hg38" in the "Select built-in genome" option and when I try to excute this message appears me: "Parameter bgenome requires a value, but has no legal values defined." Maybe, the built-in genome name (hg38) I wrote is not correct. Do you know what is the correct file name? or where can I find the names of the files? Thank you very much, Mercedes
The tool requires that the input BAM has the database assignment made. RNA STAR should be doing this at runtime, but it isn't, and that may be a bug (we are doing some testing).
Solution for now: Manually assign the database "hg38" to the input RNA STAR
bam dataset and this error will go away. There are several patch versions, so be sure to assign the primary release: Human Dec 2013 (GRCh38/hg38) (hg38)
- How do I find, adjust, and/or correct metadata? https://galaxyproject.org/support/metadata/
Thanks for reporting the issue!
Jen, Galaxy team