On 07/11/13 05:03 AM, Habib Rijzaani wrote: > Hi Seb, (Please use the mailing list, to subscribe: https://lists.sourceforge.net/lists/listinfo/denovoassembler-users )
> > I just used Ray for my small dataset with relatively high coverage reads. I > just wondering if the Coverage distribution analysis result was OK. Please > find attached. > > The analysis did not detect any peaks. Whereas, when you look at the > CoverageDistribution file, it has peak at 138 and low at 45. Is that OK, and > will that affect the results? How can I instruct Ray to use only kmer with > minimum of 45 coverage? > Since Ray 2.0.0, the peak coverage that is reported in this file (CoverageDistributionAnalysis.txt) is no longer used. Instead, the coverage distribution is locally computed for each assembly seed (that works well for metagenomes and genomes). This is described in section "From Ray to Ray Meta" in our Genome Biology paper: http://genomebiology.com/2012/13/12/R122#sec3 Séb > > *Habib Rijzaani* > > BB-Biogen, Badan Litbang Pertanian, Kementerian Pertanian > Jl. Tentara Pelajar 3A > Bogor 16111 > +62 251 8337975 ------------------------------------------------------------------------------ November Webinars for C, C++, Fortran Developers Accelerate application performance with scalable programming models. Explore techniques for threading, error checking, porting, and tuning. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk _______________________________________________ Denovoassembler-users mailing list Denovoassembler-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
