On 11/11/13 04:49 PM, JC Grenier wrote:
> Thanks for your answer. However, it could give me different results for the
> maximum Scaffold Length for example.
>
> What would you recommend in a situation where the maximum length of a contig
> is the same with either a minimum contig length of 100 or 500, but that the
> maximum scaffold length is much more bigger (~650k for 100, and 740k for
> 500)?
>
The only time where I used this parameter was to set the minimum contig length
to ( 2 * kmer length + 1 ) to avoid processing too many bubbles
on a very large dataset (white spruce).
> I suppose that the confidence is not big enough or the coverage of my sample
> is not big enough to assess clearly those contigs to this particular scaffold?
Scaffolds are built using paired information. The links used for scaffolding
are written in RayOutput/ScaffoldLinks.txt.
>Or smaller scaffolds were built with the ones that are smaller than 500bp?
You can assess which contigs are in whic scaffolds by reading this file:
RayOutput/ScaffoldComponents.txt
>
> Thanks for the clarifications.
>
>
> 2013/11/11 Sébastien Boisvert <sebastien.boisver...@ulaval.ca
> <mailto:sebastien.boisver...@ulaval.ca>>
>
> On 11/11/13 12:33 PM, JC Grenier wrote:
>
> Hi, I'm presently testing some parameters for launching Ray on
> Microbiome datasets.
>
> I have a question concerning the parameter for the minimum contig
> length.
> Can you explain me why I'm getting a lot more contigs/scaffolds > 500
> when I'm putting
> this parameter at 100 (default) than when I'm putting it at 500
> directly?
>
>
> Only assembly seeds with at least "minimum contig length" nucleotides are
> accepted.
>
> In your case, the behavior you are observing is presumably due to short
> seeds (< 500 nt)
> that are extended to longer DNA sequences (> 500 nt).
>
>
>
> Thanks a lot for your help.
>
> --
> Jean-Christophe Grenier, M.Sc.
>
> ------------------------------__-----------
> /Bio-informaticien/
> /Laboratoire de Philip Awadalla/
> /Laboratoire de Luis Barreiro/
> /CHU Sainte-Justine/
> //3175, Côte Sainte-Catherine, local B-607
> ///Tél : 514-345-4931 <tel:514-345-4931> poste 5199/
> ------------------------------__-----------
>
>
>
>
>
> --
> Jean-Christophe Grenier, M.Sc.
>
> -----------------------------------------
> /Bio-informaticien/
> /Laboratoire de Philip Awadalla/
> /Laboratoire de Luis Barreiro/
> /CHU Sainte-Justine/
> //3175, Côte Sainte-Catherine, local B-607
> ///Tél : 514-345-4931 poste 5199/
> -----------------------------------------
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