On 25/06/13 04:47 PM, Labo Derome wrote:
> assembly parameters
>
> Hi,
>
> In the assembly denovo with meta-ray, they reads are filtered or it is
> necessary to do this step with tools like fastxtoolskit?. If Meta-ray can
> filter the reads, what are the default parameters of quality?
>
> Thanks
The "Ray Meta" solution provided by the Ray program trims any character that is
not a A, T, C, or G at the start and end of any reads.
Any such character within the core of a read is converted to a A (like in
Velvet).
In my experience, it is not necessary to filter with quality values with Ray.
Sequencing errors will cause bubbles or tips.
You can visualize interactively a bubble here =>
http://genome.ulaval.ca:10241/client/?map=0§ion=1®ion=17&location=21818&depth=8&zoom=0.7
You can visualize a tip here =>
http://genome.ulaval.ca:10241/client/?map=0§ion=1®ion=17&location=11934&depth=8&zoom=0.7
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