[maker-devel] mapping annotations to a new assembly

[陈文博]

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

[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

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[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

[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