[maker-devel] [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 <carsonhh at gmail.com> 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 <jeanne.wilbrandt at web.de> 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
> >
> >
> >
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>
>
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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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