[maker-devel] map the transcripts back onto the genome using "est2genome=1"

[Quanwei Zhang]

Hello:

I am trying to annotate a new NMR genome assembly. Since the gene
annotation is available for the old version of NMR from NCBI, I tried to
map the published refSeq transcripts onto the genome by "est2genome=1".
But I found quite a few genes were lost during mapping.

Then I did another test to check the functionality of the mapping by
"est2genome=1". I mapped the published refSeq transcripts onto the old
genome (the same version for the published gene annotation) by maker with
"est2genome=1". Still I can found quite a few genes were lost during the
mapping. Below I show you the results of gene annotaion by BUSCOs,
which *annotation
completeness with single-copy orthologs*.  You can see, even we only
consider the single-copy orthologs, there are still 4% were not map back to
the genome.

Do you have any comments on this? Besides would you please give us some
suggestions to make more published gene annotation map back to the same
genome assembly through "est2genome=1"? Attached is the maker_opts.ctl file
I used for the mapping. Many thanks.

# this is the BUSCOs results using the published gene annotation
    C:99.3%[S:33.3%,D:66.0%],F:0.3%,M:0.4%,n:4104

    4077    Complete BUSCOs (C)
    1367    Complete and single-copy BUSCOs (S)
    2710    Complete and duplicated BUSCOs (D)
    14    Fragmented BUSCOs (F)
    13    Missing BUSCOs (M)
    4104    Total BUSCO groups searched

#this is the BUSCOs results using gene models after mapping by maker2.
    C:93.4%[S:36.5%,D:56.9%],F:2.6%,M:4.0%,n:4104

    3830    Complete BUSCOs (C)
    1496    Complete and single-copy BUSCOs (S)
    2334    Complete and duplicated BUSCOs (D)
    105    Fragmented BUSCOs (F)
    169    Missing BUSCOs (M)
    4104    Total BUSCO groups searched

Best
Quanwei
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