[maker-devel] multiple overlapped snoRNA genes got annotated by maker
Jia-Xing Yue
yuejiaxing at gmail.com
Fri May 26 08:20:03 MDT 2017
I see. Thanks Michael!
Best,
Jia-Xing
On Fri, May 26, 2017 at 3:54 PM, Michael Campbell <
michael.s.campbell1 at gmail.com> wrote:
> 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
>
> On May 26, 2017, at 5:28 AM, Jia-Xing Yue <yuejiaxing at gmail.com> wrote:
>
> 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/
>
>
>
--
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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