further annotate gtf file from cufflinks?

Question

[Wchang]

After Cufflinks analyses we've found some novel gene models... some with introns. I wonder if anyone knows how to proceed from here to generate a (hopefully gff3) file with ORF information (where start/stop codons are, frame of translation of each exons)?

Many thanks,
WJ

Answer 1

[eddie.im]

Take a look at this link: http://www.sequenceontology.org/gff3.shtml

It provides an example of how to create a gff file with exon/intron and alternative splicing. Hope it helps.