[maker-devel] multiple overlapped snoRNA genes got annotated by maker
Jia-Xing Yue
yuejiaxing at gmail.com
Mon May 15 11:14:26 MDT 2017
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-
> 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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>
>
>
--
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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