I already have annotated my plant genome using MAKER. I used some scripts from MAKER to recover the annotations in GFF3 format and transcripts and proteins in a fasta file. Nevertheless, I used quality_filter.pl script to clean those genes models that could result as false positive and I created a new GFF3 file to get only the gene models with an AED score of <0.5. Do you know a script to recover the proteins and transcripts from this new GFF3 file with only the good models?
Ivan PhD student UNAM