[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/

[Michael Campbell]

Hi Jia-Xing,

That has been my experience in the past as well. For the non-coding RNAs tRNA-scan is very accurate while snoscan seems to be quite sensitive but very specific. Did you give it a “snoscan_meth” file? Giving it a snoscan_meth file will help with accuracy. The biggest gains in accuracy are from small RNA-seq data. In the paper where we used snoscan on maize we didn’t keep any snoRNA predictions that didn’t have support from small RNA-seq data, in practical terms we got rid of anything with a AED of 1.

I hope this helps,

Mike

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[Jia-Xing Yue]

Hi Michael,

Many thanks for the information! I will specify the "snoscan_meth" file and give it another try then. I majorly want to use maker to annotate protein-coding genes and tRNAs. But it would be nice to have snoRNA reasonably annotated as well.

Thanks gain and have a great day!

Best,

Jia-Xing

[Jia-Xing Yue]

Hi Michael,

This is a follow-up for the snoscan issue. I found the snoscan_meth option seems have been removed in the current maker_opts.ctl template file (v2.31.9). This option used to be there according to this post (https://www.biostars.org/p/217240/). I manually specified this option in my maker_opts.ctl file but I don't think maker has correctly recognized this option:


STATUS: Parsing control files...
WARNING: Invalid option 'snoscan_meth' in control file maker_opts.ctl
...

Do you know is there a way to work around this problem? Thanks!

Best,

Jia-Xing

 

[Michael Campbell]

Hi Jia-Xing,

v2.31.9 may not have had that option. I know that it is in the v3.00.0 version, so you best option may be to update.

Thanks,

Mike

[Jia-Xing Yue]

I see. Thanks Michael!

Best,

Jia-Xing