Final Maker annotation extend ORF

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Final Maker annotation extend ORF

Xiong, Wei

Dear Developer,


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,


Wei Xiong

Ph.D. candidate | Wageningen University & Research

Plant Science Group | Biosystematics Group Radix Building 107 Droevendaalsesteeg 1

6708 PB Wageningen

The Netherlands

E-mail: [hidden email]


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