[maker-devel] mapping annotations to a new assembly

[Carson Holt]

MAKER will report back all positions. The value in the score column can be used to see how well they match the original (range between 0 and 100). In the event of a tie, you will need to manually select one or the other. The process of mapping onto a new assembly is unfortunately not completely automated. It still requires intervention  from the user in those cases.

—Carson



> On Apr 4, 2016, at 10:40 AM, 陈文博 <chenwenbo1020 at gmail.com> wrote:
> 
> Hi Carson,
> 
> Thank you. 
> 
> sorry that I forgot to mention that in the new version assembly I only connected some scaffolds into super scaffold by Ns. 
> 
> Annotation question is :
> 
> Maker use blast to anchor the gene. If some genes were mapped to multiple positions (for example single-exon genes), what will Maker decide to do?
> 
> Thanks!
> 
> Best,
> Wenbo
> 
> 2016-04-04 12:34 GMT-04:00 Carson Holt <carsonhh at gmail.com <mailto:carsonhh at gmail.com>>:
> 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 <mailto: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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> > maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>
> > http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org <http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org>
> 
> 

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