> Does RAY just use error-free reads? there are quality scores.
No, it utilise all the reads you provide.
Ray does not look at quality scores, but you can provide them nonetheless.
> 31 seems a little small for a denovo assembly, but i will try of course.
No it is not small. 4 power 31 is 4 611 686 018 427 387 904 -- more than enough
to represent the k-mers of any genomes.
Of course there will be k-mers (of length 31) in the genomes that are repeated,
but that is where paired reads help Ray.
> Can i compile RAY then with a smaller MAXKMERLENGTH option? instead of 128
> maybe 64 or even 32? even the input reads still being 101 bp long?
The default is 32. MAXKMERLENGTH is the maximum k-mer length and is not related
to the maximum read length.
The maximum read length in Ray is 65535.
Sébastien
http://github.com/sebhtml/ray
> ________________________________________
> De : [email protected] [[email protected]] de la part de Nicolas
> Balcazar [[email protected]]
> Date d'envoi : 3 septembre 2011 06:06
> À : Sébastien Boisvert
> Cc : [email protected]
> Objet : Re: RE : RE : RE : RE : RE : RE : RAY just on LAM/MPI?
>
> Does RAY just use error-free reads? there are quality scores.
> 31 seems a little small for a denovo assembly, but i will try of course.
> Can i compile RAY then with a smaller MAXKMERLENGTH option? instead of 128
> maybe 64 or even 32? even the input reads still being 101 bp long?
>
> thanks, Nicolas
>
>
>
> 2011/9/2 Sébastien Boisvert
> <[email protected]<mailto:[email protected]>>
>
>
>
> You should try with a lower k-mer length. Try -k 31.
>
> k-mers of length 101 in reads that contain no errors will not be numerous.
>
>> ________________________________________
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