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

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?

tophat rna-seq gff gtf
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updated by Biostar Biostar • written by manekineko manekineko

1 answer

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

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written by manekineko manekineko

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