[maker-devel] passing names from a gff to new predictions

[UMD Bioinformatics]

Hello

I have an interesting issue with an existing Maker gff. I have a gff file with human friendly names that I would like to pass to the new predictions. However, some of those genes in the human friendly gff file are incorrect or have errors. If I use the gff as model_gff or pred_gff with the map_forward=1 the names move but so do the incorrect models. Maker simply duplicates these predictions to the new outputs. If I remove the GFF file from the ctl file I get new predictions, that have the necessary corrections but they now have unfriendly names. Do you have any suggestions on how to associate the old names with the new predictions? I could simple blast the old proteins vs the new ones and associate them in that manor but I was wondering if there were any other options within Maker. 

Since I have the GFF files I also have the associated transcripts and proteins.
Do I need to do some iteration of est2/genome then generate a new model gff file?

The issue we are dealing with is thousands of short introns in our gff file. These are less than 20 bp and are not biologically feasible so we are trying to correct the gene model predictions.

Cheers
Ian