[Maker] Gene density threshold?

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[Maker] Gene density threshold?

Jeanne Web
Dear MAKER developers,

I have wondered whether there is an internal threshold or cutoff value
for gene density (allowing only x genes in a genomic region of a certain
size) or gene overlap (requiring to be predictions x bases apart from
each other)?

We have come to this idea when re-annotating a genome with another gene
predictor. Several cases of single-exon genes not predicted by MAKER but
flanked (i.e. close proximity) by MAKER-predictions were observed.

Thus, I'd like to ask: Which factors (apart from sequence/signals and
evidence/AED) influence the algorithmic prediction decision?

Any help is highly appreciated.
With best wishes
Jeanne Wilbrandt


~~~
Jeanne Wilbrandt, M.sc.
ORCID 0000-0002-0363-3837
~~~
PhD candidate
Leibniz PhD representative, student representative
Leibniz Graduate School on Genomic Biodiversity Research
ZFMK ~ zmb ~ University of Bonn



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Re: [Maker] Gene density threshold?

Carson Holt-2
There is no gene density parameter, and for gene overlap there is no distance parameter. Gene overlap on the same strand is not permitted though. If a gene is being excluded because of UTR overlap, you can someone correct for that by setting correct_est_fusion=1. That will trim back the UTR on those cases since this type of exclusion is often caused by false merging of neighboring transcripts during mRNA-seq assembly. Some organisms like fungi do truly have UTR overlap observed some genes, but mRNA-seq reads will assemble into a single transcript, so it’s hard to tease apart. Trimming back the UTR in those cases tends to be the most reliable solution.

—Carson


> On Dec 7, 2017, at 9:13 AM, Jeanne Web <[hidden email]> wrote:
>
> Dear MAKER developers,
>
> I have wondered whether there is an internal threshold or cutoff value for gene density (allowing only x genes in a genomic region of a certain size) or gene overlap (requiring to be predictions x bases apart from each other)?
>
> We have come to this idea when re-annotating a genome with another gene predictor. Several cases of single-exon genes not predicted by MAKER but flanked (i.e. close proximity) by MAKER-predictions were observed.
>
> Thus, I'd like to ask: Which factors (apart from sequence/signals and evidence/AED) influence the algorithmic prediction decision?
>
> Any help is highly appreciated.
> With best wishes
> Jeanne Wilbrandt
>
>
> ~~~
> Jeanne Wilbrandt, M.sc.
> ORCID 0000-0002-0363-3837
> ~~~
> PhD candidate
> Leibniz PhD representative, student representative
> Leibniz Graduate School on Genomic Biodiversity Research
> ZFMK ~ zmb ~ University of Bonn
>
>
>
> _______________________________________________
> maker-devel mailing list
> [hidden email]
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org


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Re: [Maker] Gene density threshold?

Xabier Vázquez Campos
Using the --jaccard_clip option in Trinity, also helps to reduce the merging of very close genes when assembling RNAseq. A must for fungi and other gene-dense genomes.
It increases the assembly time of RNAseq quite a lot but it is worth it.

On 8 December 2017 at 03:28, Carson Holt <[hidden email]> wrote:
There is no gene density parameter, and for gene overlap there is no distance parameter. Gene overlap on the same strand is not permitted though. If a gene is being excluded because of UTR overlap, you can someone correct for that by setting correct_est_fusion=1. That will trim back the UTR on those cases since this type of exclusion is often caused by false merging of neighboring transcripts during mRNA-seq assembly. Some organisms like fungi do truly have UTR overlap observed some genes, but mRNA-seq reads will assemble into a single transcript, so it’s hard to tease apart. Trimming back the UTR in those cases tends to be the most reliable solution.

—Carson


> On Dec 7, 2017, at 9:13 AM, Jeanne Web <[hidden email]> wrote:
>
> Dear MAKER developers,
>
> I have wondered whether there is an internal threshold or cutoff value for gene density (allowing only x genes in a genomic region of a certain size) or gene overlap (requiring to be predictions x bases apart from each other)?
>
> We have come to this idea when re-annotating a genome with another gene predictor. Several cases of single-exon genes not predicted by MAKER but flanked (i.e. close proximity) by MAKER-predictions were observed.
>
> Thus, I'd like to ask: Which factors (apart from sequence/signals and evidence/AED) influence the algorithmic prediction decision?
>
> Any help is highly appreciated.
> With best wishes
> Jeanne Wilbrandt
>
>
> ~~~
> Jeanne Wilbrandt, M.sc.
> ORCID 0000-0002-0363-3837
> ~~~
> PhD candidate
> Leibniz PhD representative, student representative
> Leibniz Graduate School on Genomic Biodiversity Research
> ZFMK ~ zmb ~ University of Bonn
>
>
>
> _______________________________________________
> maker-devel mailing list
> [hidden email]
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org


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--
Xabier Vázquez-Campos, PhD
Research Associate
NSW Systems Biology Initiative
School of Biotechnology and Biomolecular Sciences
The University of New South Wales
Sydney NSW 2052 AUSTRALIA

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Re: [Maker] Gene density threshold?

Jeanne Web

Thank you very much for the clarifications, Carson and Xabier!



On 12/08/2017 12:34 AM, Xabier Vázquez-Campos wrote:

> Using the --jaccard_clip option in Trinity, also helps to reduce the
> merging of very close genes when assembling RNAseq. A must for fungi and
> other gene-dense genomes.
> It increases the assembly time of RNAseq quite a lot but it is worth it.
>
> On 8 December 2017 at 03:28, Carson Holt <[hidden email]
> <mailto:[hidden email]>> wrote:
>
>     There is no gene density parameter, and for gene overlap there is no
>     distance parameter. Gene overlap on the same strand is not permitted
>     though. If a gene is being excluded because of UTR overlap, you can
>     someone correct for that by setting correct_est_fusion=1. That will
>     trim back the UTR on those cases since this type of exclusion is
>     often caused by false merging of neighboring transcripts during
>     mRNA-seq assembly. Some organisms like fungi do truly have UTR
>     overlap observed some genes, but mRNA-seq reads will assemble into a
>     single transcript, so it’s hard to tease apart. Trimming back the
>     UTR in those cases tends to be the most reliable solution.
>
>     —Carson
>
>
>      > On Dec 7, 2017, at 9:13 AM, Jeanne Web <[hidden email]
>     <mailto:[hidden email]>> wrote:
>      >
>      > Dear MAKER developers,
>      >
>      > I have wondered whether there is an internal threshold or cutoff
>     value for gene density (allowing only x genes in a genomic region of
>     a certain size) or gene overlap (requiring to be predictions x bases
>     apart from each other)?
>      >
>      > We have come to this idea when re-annotating a genome with
>     another gene predictor. Several cases of single-exon genes not
>     predicted by MAKER but flanked (i.e. close proximity) by
>     MAKER-predictions were observed.
>      >
>      > Thus, I'd like to ask: Which factors (apart from sequence/signals
>     and evidence/AED) influence the algorithmic prediction decision?
>      >
>      > Any help is highly appreciated.
>      > With best wishes
>      > Jeanne Wilbrandt
>      >
>      >
>      > ~~~
>      > Jeanne Wilbrandt, M.sc.
>      > ORCID 0000-0002-0363-3837
>      > ~~~
>      > PhD candidate
>      > Leibniz PhD representative, student representative
>      > Leibniz Graduate School on Genomic Biodiversity Research
>      > ZFMK ~ zmb ~ University of Bonn
>      >
>      >
>      >
>      > _______________________________________________
>      > maker-devel mailing list
>      > [hidden email]
>     <mailto:[hidden email]>
>      >
>     http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>     <http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org>
>
>
>     _______________________________________________
>     maker-devel mailing list
>     [hidden email] <mailto:[hidden email]>
>     http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>     <http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org>
>
>
>
>
> --
> Xabier Vázquez-Campos, /PhD/
> /Research Associate/
> NSW Systems Biology Initiative
> School of Biotechnology and Biomolecular Sciences
> The University of New South Wales
> Sydney NSW 2052 AUSTRALIA


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