[maker-devel] multiple overlapped snoRNA genes got annotated by maker

[Jia-Xing Yue]

Hello,

I configured snoscan (v.0.9.1) for my maker installation (v2.31.9) and run
the annotation for a yeast (S. cerevisiae) genome. I think the annotation
went well with regard to tRNAs and protein-coding genes but I am not sure
about snoRNAs. I found multiple overlapped snoRNA genes were annotated by
maker as the example below shows. I was wondering if this is expected. If
not, what might have caused this problem and is there a way to work around.
Thanks in advance!

chrIX   maker   gene    4328    4416    .       +       .
ID=snoscan-chrIX-noncoding-gene-0.49;Name=snoscan-chrIX-noncoding-gene-0.49
chrIX   maker   snoRNA  4328    4416    .       +       .
ID=snoscan-chrIX-noncoding-gene-0.49-snoRNA-1;Parent=snoscan-chrIX-noncoding-gene-0.49;Name=snoscan-chrIX-noncoding-gene-0.49-snoRNA-1;_AED=1.00;_eAED=1.00;_QI=0|-1|0|0|-1|0|1|90|0
chrIX   maker   exon    4328    4416    .       +       .
ID=snoscan-chrIX-noncoding-gene-0.49-snoRNA-1:exon:12260;Parent=snoscan-chrIX-noncoding-gene-0.49-snoRNA-1
chrIX   maker   gene    4375    4563    .       +       .
ID=snoscan-chrIX-noncoding-gene-0.50;Name=snoscan-chrIX-noncoding-gene-0.50
chrIX   maker   snoRNA  4375    4563    .       +       .
ID=snoscan-chrIX-noncoding-gene-0.50-snoRNA-1;Parent=snoscan-chrIX-noncoding-gene-0.50;Name=snoscan-chrIX-noncoding-gene-0.50-snoRNA-1;_AED=1.00;_eAED=1.00;_QI=0|-1|0|0|-1|0|1|190|0
chrIX   maker   exon    4375    4563    .       +       .
ID=snoscan-chrIX-noncoding-gene-0.50-snoRNA-1:exon:12261;Parent=snoscan-chrIX-noncoding-gene-0.50-snoRNA-1
chrIX   maker   gene    4375    4461    .       +       .
ID=snoscan-chrIX-noncoding-gene-0.51;Name=snoscan-chrIX-noncoding-gene-0.51
chrIX   maker   snoRNA  4375    4461    .       +       .
ID=snoscan-chrIX-noncoding-gene-0.51-snoRNA-1;Parent=snoscan-chrIX-noncoding-gene-0.51;Name=snoscan-chrIX-noncoding-gene-0.51-snoRNA-1;_AED=1.00;_eAED=1.00;_QI=0|-1|0|0|-1|0|1|88|0
chrIX   maker   exon    4375    4461    .       +       .
ID=snoscan-chrIX-noncoding-gene-0.51-snoRNA-1:exon:12262;Parent=snoscan-chrIX-noncoding-gene-0.51-snoRNA-1
chrIX   maker   gene    4375    4491    .       +       .
ID=snoscan-chrIX-noncoding-gene-0.52;Name=snoscan-chrIX-noncoding-gene-0.52
chrIX   maker   snoRNA  4375    4491    .       +       .
ID=snoscan-chrIX-noncoding-gene-0.52-snoRNA-1;Parent=snoscan-chrIX-noncoding-gene-0.52;Name=snoscan-chrIX-noncoding-gene-0.52-snoRNA-1;_AED=1.00;_eAED=1.00;_QI=0|-1|0|0|-1|0|1|118|0
chrIX   maker   exon    4375    4491    .       +       .
ID=snoscan-chrIX-noncoding-gene-0.52-snoRNA-1:exon:12263;Parent=snoscan-chrIX-noncoding-gene-0.52-snoRNA-1
chrIX   maker   gene    4375    4500    .       +       .
ID=snoscan-chrIX-noncoding-gene-0.53;Name=snoscan-chrIX-noncoding-gene-0.53
chrIX   maker   snoRNA  4375    4500    .       +       .
ID=snoscan-chrIX-noncoding-gene-0.53-snoRNA-1;Parent=snoscan-chrIX-noncoding-gene-0.53;Name=snoscan-chrIX-noncoding-gene-0.53-snoRNA-1;_AED=1.00;_eAED=1.00;_QI=0|-1|0|0|-1|0|1|127|0
chrIX   maker   exon    4375    4500    .       +       .
ID=snoscan-chrIX-noncoding-gene-0.53-snoRNA-1:exon:12264;Parent=snoscan-chrIX-noncoding-gene-0.53-snoRNA-1

Best,
Jia-Xing


-- 
Jia-Xing Yue

Population Genomics and Complex Traits Group
Tour Pasteur 8eme etage
Faculté de Médecine
Institute for Research on Cancer and Aging, Nice (IRCAN)
CNRS UMR 7284 - INSERM U 1081 - Université Côte d’Azur (UCA)
28 Avenue de Valombrose
06107 NICE Cedex 2
France

Personal website: http://www.iamphioxus.org/
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