GFF3 file format for TopHat

[shurjo]

Hello everyone,

I just used gtf2gff3 to convert the UCSC knownGenes GTF file to GFF3 format and would like to use this as the supplied annotation for a TopHat run. Now, according to the TopHat manual, "Transcript records are called "mRNA", not "transcript"." However, in the GFF3 file I just created, both the "mRNA" and "transcript" SOFA terms are present. Specifically, here are the counts:

488996 CDS
612391 exon
93721 five_prime_utr
66803 gene
53036 mRNA
53036 start_codon
13767 transcript

Does anyone have experience with this situation and can tell me if TopHat will work with this file?

Thanks,

Shurjo