On 26.02.2014 15:02, David Eccles (gringer) wrote: > I have no idea if this peak coverage problem will impact how Ray deals with > the assembly. If it does, I'll probably need to do some > kmer-based error correction prior to assembly with Ray in the hope that it > will bring those kmers with coverage 2-20 down to frequencies > below the true peak value.
So, I've now used BayesHammer (i.e. SPAdes) for error correction, and selected only samples that were from the same strain, but the coverage problem still remains. Because the counts at 2X are larger than the counts at ~500X, 2 is chosen for the peak coverage: CoverageDistribution.postEC.txt CoverageDistributionAnalysis.postEC.txt [these are from 250bp paired-end Illumina reads] I'll try again with a larger kmer size. I guess that might cause a few more of those reads to become unique. - David ------------------------------------------------------------------------------ Flow-based real-time traffic analytics software. Cisco certified tool. Monitor traffic, SLAs, QoS, Medianet, WAAS etc. with NetFlow Analyzer Customize your own dashboards, set traffic alerts and generate reports. Network behavioral analysis & security monitoring. All-in-one tool. http://pubads.g.doubleclick.net/gampad/clk?id=126839071&iu=/4140/ostg.clktrk _______________________________________________ Denovoassembler-users mailing list Denovoassembler-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
