[maker-devel] mapping annotations to a new assembly

[Carson Holt]

Because the assembly has changed. That means that sequence can be different, missing, or altered to break previous CDS. You can try relaxing the filtering parameters in maker_bopts.ctl to recover more partial or incomplete matches. Also adjust the mx intron size to allow for really long introns. That might recover a few more.

—Carson



> On Apr 2, 2016, at 5:41 PM, 陈文博 <chenwenbo1020 at gmail.com> wrote:
> 
> Hi All,
> 
> Recently, I updated the genome assembly, and want to update the annotation to fit the new genome, only want to update the gene position. I used Maker. I changed the maker_opt.ctl file as follow:
> 
> genome=$PATH_TO_mygenome
> 
> organism_type=eukaryotic 
> 
> est=$PATH_TO_transcript_seq
> 
> est2genome=1
> 
> 
> est_forward=1
> 
> After run Maker, some genes were lost. There are 14,146 transcritpts as input. Only 13092 gene models were in the output. Anyone know the reason? Thank you!
> 
> Best regards,
> Wenbo
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