I'm trying to run cuffdiff with bias correction:
perform bias correction 'yes' -> Reference sequence data 'locally cached' -> Using Reference Genome
I have run cuffdiff previously with this option selected and I was able to select "Mouse(Mus Musculus) mm10." However, now mm10 first shows up for a bit with a spinner circle, then goes to "no options available."
I have seen this github thread about the same error in cuffmerge: https://github.com/galaxyproject/galaxy/issues/388, and it seems like there is no solution yet?
Below shows the parameters from before, when I was able to select the mm10:
Transcripts Cuffmerge on data 262, data 1077, and others: merged transcripts Omit Tabular Datasets False Generate SQLite True Library normalization method geometric Dispersion estimation method pooled False Discovery Rate 0.05 Min Alignment Count 10 Use multi-read correct True Perform Bias Correction Yes Reference sequence data cached Using reference genome **mm10** Include Read Group Datasets Yes Include Count Based output files Yes apply length correction cufflinks effective length correction Set Additional Parameters for single end reads? (not recommended for paired-end reads) No Set Advanced Cuffdiff parameters? No Job Resource Parameters no
Now I am unable to select 'mm10' under locally cached sequence data. I'm wondering why what was once available is not anymore.