Hello,
But N/4 reads will likely contain all the things that diginorms would weed out,
right ?
Does diginorm works with read paths in the de Bruijn stored in its Bloom filter
?
If not, not only diginorm does not use pairs, but it does not use read
threading
neither.
Sébastien
On 16/09/12 07:37 PM, Torsten Seemann wrote:
> Does anyone know if Ray would be compatible with diginorm?
> http://arxiv.org/abs/1203.4802
> I ask because I'm not sure if the normalisation process outlined in the
> paper would mess with the determination of graph loops by Ray.
>
>
> Titus's diginorm is very cool, but it currently has some caveats:
>
> - it doesn't work with paired-end reads yet
> - the normalization process throws away all repeat information
>
> You may be better off just sub-sampling your read file. ie. if N reads, use
> first N/4 of them.
>
> --
> --Torsten Seemann
> --Victorian Bioinformatics Consortium, Dept. Microbiology, Monash University,
> AUSTRALIA
>
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