Cuffmerge Exon vs Transcript output from Cufflinks Problem.

[tonup69]

One issue I continue to have is that Cufflinks output contains both "transcript" and "exon" lines which, in some cases, match the same gene ID and coordinates. Cuffmerge is seeing this as an error (i.e. it sees duplicate genes and fails). I did a work around by selecting just exon level data for cuffmerge, but now my cuffdiff output does NOT have CDS tables (as expected). Can I still build a database for CummeRbund or is there some other work around I should use.

Using updated Cufflinks and Cuffmerge tools 2.2.1.0 in our GALAXY install.