3.0 years ago by
Examine the reference annotation dataset being used or consider using one (GFF3 or GTF dataset).
There are specific attributes in reference annotation datasets that this tool package uses to populate these values with meaningful content. The idea is to make certain that the annotation is both an exact match for the reference genome used in the prior mapping step and that it contains those key attributes in order for the annotation to populate into the tool output. Full details here in the manual
If your genome is supported, the GTF from iGenomes can be used with the Tuxedo RNA-seq analysis tools (Tophat, Cufflinks, Cuffdiff, etc). The iGenomes genes.gtf dataset contains all of the extra attributes that enable full functionality. There are also other annotation sources depending on the genome.
Best, Jen, Galaxy team