[maker-devel] Help with updating an annotation

[Saad Arif]

Dear All,

I would like to use Maker pipeline  to expand a current annotation (new isoforms and novel genes with respect to current annotation) and was wondering if anyone had experience with this and or suggestions to my questions.

Briefly:

 I have tophat splice junctions from RNAseq data or alternatively cufflinks generated transcript models (fasts format) that i want to use as my new data (est_gff or est). 

I want to provide the current Ensembl annotation for gene prediction but i want this annotation to remain unchanged. Hence, i’m not sure if i should provide this annotation as pred_gff
 or model_gff. Can the model_gff be used for gene prediction or is this just a subset of pred_gff that remain unaltered? Can we provide the same annotation for both options (pred_ and mod_gff)?



Importantly, my main goal is to use the new RNAseq data to add more isoforms and (any) novel genes to the existing Ensembl annotation. Any thoughts or suggestions on how to go about  this would be  sincerely appreciated.


Thanks in advance,
saad