[maker-devel] Incorporating cufflinks in maker

[Holmer, Rens]

Hi maker team,

I am currently working on a project where we want to incorporate quite a lot of RNA-seq into our annotation. Currently I see two options:

Provide the cufflinks output as EST-gff
Process cufflinks output with TransDecoder (find ORFs, annotate UTR, etc) and provide this as either pred_gff or model_gff

What would you suggest, and what would be the required formatting for both options?

Thanks in advance,

Rens Holmer