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)?
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? Or smaller scaffolds were built with the ones that are smaller
than 500bp?
Thanks for the clarifications.
2013/11/11 Sébastien Boisvert <[email protected]>
> 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 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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