On Tue, Sep 6, 2011 at 9:29 PM, Peng, Tao firstname.lastname@example.org wrote:
Hi I had 3 GTF files from ensemble, UCSC and NCBI for annotation; ONLY ensemble were recognized by GALAXY cufflinks as a GTF file although they all have .GTF. I am NOT sure why UCSC and NCBI GTF files were seen as GFF files?
I'm pretty sure Galaxy ignores the original filename extension (it will be stored on disk as *.dat once uploaded to Galaxy).
If you could post the start of each file (or links to the complete files) that would be very helpful for working out why Galaxy has misidentified the GTF files as GFF.