I have a de novo transcriptome file and partial genome file which I need to make a (GFF/GTF) annotation map based on both transcriptome and draft genome information.
I have includes both scaffolds from Trinity and StringTie in order to make a comprehensive transcriptome. Nqow I need to make annotation based on both draft partial genome file and assembled transcriptome.
1- I have tried Pasa which mostly used GMAP, but is there any other pipeline for such purpose?
2- How can perform this process by myself with just applying softwares not pipelines?
Thanks for consideration and help.