gff format to genome annotation

Question

[h.mon]

I am mapping RNAseq transcripts against a genome to annotate it. I am looking at Spaln and GMAP, and they both have two types of gff files as output (GFF3 gene format and GFF3 match format), which one is better to proceed with annotation? What is the difference between them?

Related question: is gff the best output to proceed with annotation?

[ben@f]

Hi, I have the same doubt, How can I align a set of proteins to an eukaryotic-size genome in order to generate a GFF3 gene format that is compatible with evidence modeler.. any suggestions or hint is very appreciated. Thank you