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

Jia-Xing Yue yuejiaxing at gmail.com
Fri May 26 03:28:48 MDT 2017 

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



On Mon, May 15, 2017 at 7:14 PM, Jia-Xing Yue <yuejiaxing at gmail.com> wrote:

> 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
>
>
> On Mon, May 15, 2017 at 6:28 PM, Michael Campbell <
> michael.s.campbell1 at gmail.com> wrote:
>
>> 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
>>
>> On May 15, 2017, at 7:28 AM, Jia-Xing Yue <yuejiaxing at gmail.com> wrote:
>>
>> 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-nonc
>> oding-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;Par
>> ent=snoscan-chrIX-noncoding-gene-0.49-snoRNA-1
>> chrIX   maker   gene    4375    4563    .       +       .
>> ID=snoscan-chrIX-noncoding-gene-0.50;Name=snoscan-chrIX-nonc
>> oding-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;Par
>> ent=snoscan-chrIX-noncoding-gene-0.50-snoRNA-1
>> chrIX   maker   gene    4375    4461    .       +       .
>> ID=snoscan-chrIX-noncoding-gene-0.51;Name=snoscan-chrIX-nonc
>> oding-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;Par
>> ent=snoscan-chrIX-noncoding-gene-0.51-snoRNA-1
>> chrIX   maker   gene    4375    4491    .       +       .
>> ID=snoscan-chrIX-noncoding-gene-0.52;Name=snoscan-chrIX-nonc
>> oding-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;Par
>> ent=snoscan-chrIX-noncoding-gene-0.52-snoRNA-1
>> chrIX   maker   gene    4375    4500    .       +       .
>> ID=snoscan-chrIX-noncoding-gene-0.53;Name=snoscan-chrIX-nonc
>> oding-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;Par
>> ent=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/
>>
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>
>>
>>
>
>
> --
> 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/
>
>


-- 
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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