GFF problem - gtf_to_fasta (Tophat) outputs only 2 sequences from 70 entries in GFF?

Question

[manekineko]

Hi,

I have a GFF that made and validate via Online GFF validator, double and triple check it, but from 70 entries gtf_to_fasta (Tophat) outputs only 2 sequences,

Also When I want to Make GFF to GTF the gtfread (Cufflinks) also outputs only 2 entries in the GTF file?! So cannot see where is the problem with my GFF?

Answer 1

[manekineko]

Is there a specific requirements for the GFF that tophat needs? I just have putative regions (e.g. chromosome start stop strand name)?