Final Maker annotation extend ORF

classic Classic list List threaded Threaded
1 message Options
Reply | Threaded
Open this post in threaded view
|

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]

 


_______________________________________________
maker-devel mailing list
[hidden email]
http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org