How does Ray deal with the mixture of correct (<-- -->, large span) and
noise (--> <--, short span) reads found in a typical mate pair library? Is
it explicitly partitioning/classifying the reads into these categories?
On Tue, Feb 12, 2013 at 8:54 AM, Sébastien Boisvert <
[email protected]> wrote:
>
>
> On 02/12/2013 05:15 AM, frederic texier wrote:
> > Bonjour de nouveau,
> >
> > J'ai un problème quand je veux installer avec l'otpion HAVE_LIBZ=y.
> > Faut-il un module supplémentaire à installer avant?
> >
>
> Yes, you need zlib headers.
>
> On Debian or Ubuntu or other Debian-derived distributions:
>
> sudo apt-get install -y zlib1g-dev
>
>
> On Fedora or CentOS or other similar distribution:
>
> sudo yum install -y zlib-devel
>
>
> There is also the option HAVE_LIBBZ2=y that provides native support for
> fastq.bz2 files.
>
> > Je vous remercie.
> > Cordialement
> > Frédéric Texier.
> >
> > -----Message d'origine-----
> > De : Sébastien Boisvert [mailto:[email protected]]
> > Envoyé : vendredi 8 février 2013 18:05
> > À : frederic texier
> > Cc : [email protected]
> > Objet : Re: Ray output
> >
> > Bonjour Frédéric,
> >
> > There is a work-in-progress to add this feature [1], although it's not in
> > the current backlog [2].
> >
> > Current available courses of action are:
> >
> > 1. use -amos option to generate a AMOS file with Ray and then parse this
> to
> > obtain the information you want (used reads, and so on).
> >
> > 2. Map your reads on contigs (or on scaffolds) with a aligner and then
> pipe
> > this in a existing tool (I am sure there exists tools for that that take
> a
> > SAM file as input).
> >
> >
> > Also, if you want to visualize your assemblies to do some quality
> controls
> > (usually production departments like to do quality controls), you can use
> > Ray Cloud Browser.
> >
> >
> > Demo: http://genome.ulaval.ca/corbeillab/Ray-Cloud-Browser/
> > Source code: https://github.com/sebhtml/Ray-Cloud-Browser
> > Deployment instructions:
> >
> https://raw.github.com/sebhtml/Ray-Cloud-Browser/master/Documentation/Deploy
> > ment.txt
> >
> >
> > ---
> > [1] https://github.com/sebhtml/ray/issues/65
> > [2] https://github.com/sebhtml/ray/issues?milestone=5&state=open
> >
> >
> >
> >
> > Sébastien Boisvert
> > Community Manager, Ray Genomics Software Suite PhD student, Université
> Laval
> >
> > On 02/08/2013 09:05 AM, frederic texier wrote:
> >> Hello,
> >>
> >> I have used Ray to assemble bacterial genome but I don't know where find
> > the number of reads really used and the numer of reads not used in the
> > output.
> >>
> >> could you help me to find this, please?
> >>
> >> Thank you.
> >> --
> >>
> >> Frédéric Texier
> >>
> >> Téléphone: +33(0)359317403
> >> E-mail: [email protected]
> >>
> >> Genoscreen
> >> Campus Pasteur - 1 rue du Pr Calmette
> >> 59000 Lille
> >> Téléphone: +33(0)320877153
> >>
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