[maker-devel] mapping annotations to a new assembly

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陈文博

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Apr 2, 2016, 7:41:40 PM4/2/16
to maker...@yandell-lab.org
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

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Apr 4, 2016, 12:35:02 PM4/4/16
to 陈文博, maker...@yandell-lab.org
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

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Apr 4, 2016, 12:40:48 PM4/4/16
to Carson Holt, maker...@yandell-lab.org
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

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Apr 4, 2016, 12:43:12 PM4/4/16
to 陈文博, maker...@yandell-lab.org
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
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