I recently tried differential gene expression analysis using an established workflow. I had miRNA data of two conditions, single replicate. I fed my fastqsanger data and the reference genome I called from UCSC, into the workflow. Galaxy did generate a Cuffdiff SQlite database but when I use it to get plots with cummerbund tool, I receive the error below:
cummerbund tool error "Attempting to run a tool with empty command definition."
The workflow I used is; DEG:Tuxedo2 - 2 Conditions 1 Replicate each
What do you think is the problem? Thank you!! Efraim
EDIT: I just checked the other data generated by the workflow and I have two other errors from Cufflinks and Cuffmerge; "An error occurred setting the metadata for this dataset Set it manually or retry auto-detection" Could they be connected?