I have used MAKER to annotate my genome. The input for MAKER run is pred_gff (de-novo annotation by Augustus), the protein sequence of a close species, and an assembled Transcriptome by RNA-seq using Trinity.
When I checked the output, I noticed that many of the predicted gene models are with extended the regions flanking the ORF.
I have checked the evidence I applied. I think the Transcriptome data is the reason because the RNA-seq not only contain the matured mRNA
My question is, how can I properly make use of the mRNA while preventing this extension? Is there any way I can fix the current annotation instead of re-run the annotation?
Thank you for your help. I look forward to hearing from you!
Best regards and stay safe,
Ph.D. candidate | Wageningen University & Research
Plant Science Group | Biosystematics Group Radix Building 107 Droevendaalsesteeg 1