I'm using cufflink on Galaxy. It only uses gff3 or gtf.
I feel there are no differences among gff3, gff2 and gff. The attribute part differs a little bit but does that really matter?
Also I used STAR, which mostly takes gtf file. Is there anyone successfully using .gff in STAR?
Thanks!
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My gff file is like this:
scaffold_1000 EVM gene 2619 5087 . - . ID=pgl1000.1
scaffold_1000 EVM mRNA 2619 5087 . - . ID=pgl1000.1;Parent=pgl1000.1
scaffold_1000 EVM exon 5002 5087 . - . ID=pgl1000.1.exon1;Parent=pgl1000.1
scaffold_1000 EVM CDS 5002 5087 . - 0 ID=cds.pgl1000.1;Parent=pgl1000.1
scaffold_1000 EVM exon 2619 2838 . - . ID=pgl1000.1.exon2;Parent=pgl1000.1