Greetings, I am trying to use the Cufflinks tool in the main/public instance of Galaxy to generate FPKMs for my BAM files against hg38. The tool throws an error having to do with the locally cached hg38 reference. Below I include the steps to reproduce the error with BAM files aligned to hg38.
In the main Cufflinks options, when in 'Perform Bias Correction', I enter 'yes', and in 'Reference sequence data', I enter 'locally cached', and in 'Using reference genome' I select 'hg38',
when I click 'Execute'- I get the following error message:
"An invalid option was selected for index, u'hg38', please verify" .
Again, the error indicates the problem is with the locally (Galaxy) cached hg38 reference (or code to access it), not a file I've uploaded or pulled from UCSC GB.
Thanks so much! Apologizes in advanced if my blunder is obvious.