[maker-devel] mapping annotations to a new assembly

[陈文博]

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>:

> 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
> > _______________________________________________
> > maker-devel mailing list
> > maker-devel at yandell-lab.org
> > http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org
>
>
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