Hi,

I've downloaded two GTF files based on the Ensembl annotation, both of which fail when running gffread -E on them, stating that it cannot parse.

Ensembl Homo Sapiens - http://cufflinks.cbcb.umd.edu/igenomes.html (Using the genes.gtf from the annotation directory) - http://www.ensembl.org/info/data/ftp/index.html (GTF Gene Set)

I've ran the Tophat -> Cufflinks pipes so far, and when getting to the Cuffmerge stage, I get a duplicate entry error. I grepped the annotation GTF file and there doesn't appear to be any duplicates.

If anyone has any suggestions it'd be greatly appreciated, thanks!