Is it possible to extract the GFF3 file for the raw gene models predicted by est2genome and protein2genome?

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Is it possible to extract the GFF3 file for the raw gene models predicted by est2genome and protein2genome?

Jia-Xing Yue-2
Hello,

I enabled the est2genome and protein2genome option for Maker-3.00.0-beta in my particular case. I was wondering if it is possible to extract the gene models predicted by snap, augustus, est2genome, and protein2genome respectively.

By using the gff_merge command, I think I can extract some gene models for each cases but not all, especially for the est2genome and protein2genome set (e.g. those labeled with "maker-chr*-exonerate_est2genome-gene" and "maker-chr*-exonerate_protein2genome-gene").

Thanks in advance!

Best,
Jia-Xing




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Re: Is it possible to extract the GFF3 file for the raw gene models predicted by est2genome and protein2genome?

Carson Holt-2
You can just grep on the name. Although est2genome and protein2genome should only be used for initial training, as they are almost always guaranteed to be partial and should be disabled once you have trained gene predictors that can build complete models.

—Carson

> On Jan 30, 2018, at 9:32 AM, Jia-Xing Yue <[hidden email]> wrote:
>
> Hello,
>
> I enabled the est2genome and protein2genome option for Maker-3.00.0-beta in my particular case. I was wondering if it is possible to extract the gene models predicted by snap, augustus, est2genome, and protein2genome respectively.
>
> By using the gff_merge command, I think I can extract some gene models for each cases but not all, especially for the est2genome and protein2genome set (e.g. those labeled with "maker-chr*-exonerate_est2genome-gene" and "maker-chr*-exonerate_protein2genome-gene").
>
> Thanks in advance!
>
> Best,
> Jia-Xing
>
>
>
> _______________________________________________
> maker-devel mailing list
> [hidden email]
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org


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Re: Is it possible to extract the GFF3 file for the raw gene models predicted by est2genome and protein2genome?

Jia-Xing Yue-2
Dear Carson,

Thanks for the quick response! Could you elaborate  a bit on on "grep on the name". Do you mean just grep all the lines in the gff_merge output with "est2genome" and "protein2genome" in column 3? In that case, what I got is the alignments rather than the gene model guessed by Maker based on the alignment, right?


Thanks!

Best,
Jia-Xing



On Tue, Jan 30, 2018 at 5:57 PM, Carson Holt <[hidden email]> wrote:
You can just grep on the name. Although est2genome and protein2genome should only be used for initial training, as they are almost always guaranteed to be partial and should be disabled once you have trained gene predictors that can build complete models.

—Carson

> On Jan 30, 2018, at 9:32 AM, Jia-Xing Yue <[hidden email]> wrote:
>
> Hello,
>
> I enabled the est2genome and protein2genome option for Maker-3.00.0-beta in my particular case. I was wondering if it is possible to extract the gene models predicted by snap, augustus, est2genome, and protein2genome respectively.
>
> By using the gff_merge command, I think I can extract some gene models for each cases but not all, especially for the est2genome and protein2genome set (e.g. those labeled with "maker-chr*-exonerate_est2genome-gene" and "maker-chr*-exonerate_protein2genome-gene").
>
> Thanks in advance!
>
> Best,
> Jia-Xing
>
>
>
> _______________________________________________
> maker-devel mailing list
> [hidden email]
> 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

Twitter: @iAmphioxus

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Re: Is it possible to extract the GFF3 file for the raw gene models predicted by est2genome and protein2genome?

Carson Holt-2
MAKER models will al have ‘maker’ in the source column. Everything else is a reference alignment (not a model). But you can grep on the gene name. If it is sourced from SNAP, it will have snap in the name, and the same is true for augustus, est2genome, protein2genome, etc.

—Carson


On Jan 30, 2018, at 10:03 AM, Jia-Xing Yue <[hidden email]> wrote:

Dear Carson,

Thanks for the quick response! Could you elaborate  a bit on on "grep on the name". Do you mean just grep all the lines in the gff_merge output with "est2genome" and "protein2genome" in column 3? In that case, what I got is the alignments rather than the gene model guessed by Maker based on the alignment, right?


Thanks!

Best,
Jia-Xing



On Tue, Jan 30, 2018 at 5:57 PM, Carson Holt <[hidden email]> wrote:
You can just grep on the name. Although est2genome and protein2genome should only be used for initial training, as they are almost always guaranteed to be partial and should be disabled once you have trained gene predictors that can build complete models.

—Carson

> On Jan 30, 2018, at 9:32 AM, Jia-Xing Yue <[hidden email]> wrote:
>
> Hello,
>
> I enabled the est2genome and protein2genome option for Maker-3.00.0-beta in my particular case. I was wondering if it is possible to extract the gene models predicted by snap, augustus, est2genome, and protein2genome respectively.
>
> By using the gff_merge command, I think I can extract some gene models for each cases but not all, especially for the est2genome and protein2genome set (e.g. those labeled with "maker-chr*-exonerate_est2genome-gene" and "maker-chr*-exonerate_protein2genome-gene").
>
> Thanks in advance!
>
> Best,
> Jia-Xing
>
>
>
> _______________________________________________
> maker-devel mailing list
> [hidden email]
> 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

Twitter: @iAmphioxus


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[hidden email]
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Re: Is it possible to extract the GFF3 file for the raw gene models predicted by est2genome and protein2genome?

Jia-Xing Yue-2
In reply to this post by Jia-Xing Yue-2
Dear Carson,

Yes that's what I did actually. But it seems that I  only got much fewer gene models for est2genome and protein2genome in this way than I  would expect. I have turned on EVM for my maker run. Could this explain the low numbers of est2genome and protein2genome models    that I got? Thx!

Best,
Jia-Xing

Sent from my Nokia Lumia 920

From: [hidden email]
Sent: ‎30/‎01/‎2018 18:06
To: [hidden email]
Cc: [hidden email]
Subject: Re: [maker-devel] Is it possible to extract the GFF3 file for the raw gene models predicted by est2genome and protein2genome?

MAKER models will al have ‘maker’ in the source column. Everything else is a reference alignment (not a model). But you can grep on the gene name. If it is sourced from SNAP, it will have snap in the name, and the same is true for augustus, est2genome, protein2genome, etc.

—Carson


On Jan 30, 2018, at 10:03 AM, Jia-Xing Yue <[hidden email]> wrote:

Dear Carson,

Thanks for the quick response! Could you elaborate  a bit on on "grep on the name". Do you mean just grep all the lines in the gff_merge output with "est2genome" and "protein2genome" in column 3? In that case, what I got is the alignments rather than the gene model guessed by Maker based on the alignment, right?


Thanks!

Best,
Jia-Xing



On Tue, Jan 30, 2018 at 5:57 PM, Carson Holt <[hidden email]> wrote:
You can just grep on the name. Although est2genome and protein2genome should only be used for initial training, as they are almost always guaranteed to be partial and should be disabled once you have trained gene predictors that can build complete models.

—Carson

> On Jan 30, 2018, at 9:32 AM, Jia-Xing Yue <[hidden email]> wrote:
>
> Hello,
>
> I enabled the est2genome and protein2genome option for Maker-3.00.0-beta in my particular case. I was wondering if it is possible to extract the gene models predicted by snap, augustus, est2genome, and protein2genome respectively.
>
> By using the gff_merge command, I think I can extract some gene models for each cases but not all, especially for the est2genome and protein2genome set (e.g. those labeled with "maker-chr*-exonerate_est2genome-gene" and "maker-chr*-exonerate_protein2genome-gene").
>
> Thanks in advance!
>
> Best,
> Jia-Xing
>
>
>
> _______________________________________________
> maker-devel mailing list
> [hidden email]
> 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

Twitter: @iAmphioxus


_______________________________________________
maker-devel mailing list
[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org