[maker-devel] [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 <carsonhh at gmail.com 
> <mailto: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
>     <mailto: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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> 
> 
> -- 
> 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