FR, and around 200 (Id have to double check though). On Wed, Sep 26, 2012 at 3:40 AM, Sébastien Boisvert <sebastien.boisver...@ulaval.ca> wrote: > Hello, > > What is the strand orientation of your fosmid data ? > > And what is the expected insert size (including both read lengths and > gap) ? > > On 25/09/12 07:07 PM, Adam Caldwell wrote: >> On Mon, Sep 24, 2012 at 12:44 PM, Sébastien Boisvert >> <sebastien.boisver...@ulaval.ca> wrote: >>> Hello, >>> >>> On 24/09/12 03:30 PM, Adam Caldwell wrote: >>>> On Mon, Sep 24, 2012 at 5:47 AM, Sébastien Boisvert >>>> <sebastien.boisver...@ulaval.ca> wrote: >>>>> Hello, >>>>> >>>>> On 22/09/12 01:28 AM, Adam Caldwell wrote: >>>>>> Is there any documentation for the metagenomic assembly abilities of >>>>>> Ray? I couldnt find any. >>>>> >>>>> We have a paper that we need to resend in revised form about Ray Méta (de >>>>> novo >>>>> metagenome assembly) and Ray Communities (biological abundances and >>>>> taxonomic profiling). >>>>> >>>>>> The reason I ask is it performs surprisingly >>>>>> poorly on my data. >>>>> >>>>> What type of data exactly ? >>>> >>>> These are pools of several hundred fosmids (~40kb pieces), sequenced >>>> with Illumina. They are 2x75bp, paired end. While this is similar to a >>>> metagenomic project in that there are hundreds on different species >>>> sequenced together, each clone should have roughly equal coverage. I >>>> have good assemblies with Velvet/MetaVelvet and ABySS, so it is >>>> curious that Ray doesnt come close, when it works so well for single >>>> genomes. >>>> >>> >>> What k-mer length are you using ? >>> >>> Does Ray detect paired information correctly for your input data >>> (look in LibraryStatistics.txt) >> >> I tried 31 and 41, with 41 giving slightly better results. Paired >> reads seem to be detected: >> >> NumberOfPairedLibraries: 1 >> >> LibraryNumber: 0 >> InputFormat: TwoFiles,Paired >> DetectionType: Automatic >> File: reads_archive/lane1a_reads/lane1a_novec_paired.1.fastq >> NumberOfSequences: 7595472 >> File: reads_archive/lane1a_reads/lane1a_novec_paired.2.fastq >> NumberOfSequences: 7595472 >> Distribution: lane1a_ray41/Library0.txt >> Peak 0 >> AverageOuterDistance: 93 >> StandardDeviation: 33 >> >>> >>>> I take it from your response, there is no specific flag to enable a >>>> metagenomic mode? Does Ray somehow detect whether a sample is single >>>> or metagenome, or has the algorithm just been tuned to handle both >>>> types equally well? >>>> >>> >>> Indeed, the new code handles both single-genome multiple-cell assembly and >>> multiple-genome multiple-cell assemblies. >>> >>> It is a generalization, if you will. >> >> Seems there isnt much I can do, then. Not really a worry, I was just >> trying to evaluate an assortment of assemblers for this project, and >> it seems others are better suited. >> >>> >>>>> >>>>>> Multiple other assemblers had a N50 an order of >>>>>> magnitude higher, and largest contigs over twice as long. >>>>>> >>>>>> I am assuming I am missing something, or perhaps its not completely >>>>>> implemented? Im using Ray cloned from git today. >>>>>> >>>>>> ------------------------------------------------------------------------------ >>>>>> How fast is your code? >>>>>> 3 out of 4 devs don\\\'t know how their code performs in production. >>>>>> Find out how slow your code is with AppDynamics Lite. >>>>>> http://ad.doubleclick.net/clk;262219672;13503038;z? >>>>>> http://info.appdynamics.com/FreeJavaPerformanceDownload.html >>>>>> _______________________________________________ >>>>>> Denovoassembler-users mailing list >>>>>> Denovoassembler-users@lists.sourceforge.net >>>>>> https://lists.sourceforge.net/lists/listinfo/denovoassembler-users >>>>> >>>>> >>>>> >>>>> ------------------------------------------------------------------------------ >>>>> Live Security Virtual Conference >>>>> Exclusive live event will cover all the ways today's security and >>>>> threat landscape has changed and how IT managers can respond. Discussions >>>>> will include endpoint security, mobile security and the latest in malware >>>>> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ >>>>> _______________________________________________ >>>>> Denovoassembler-users mailing list >>>>> Denovoassembler-users@lists.sourceforge.net >>>>> https://lists.sourceforge.net/lists/listinfo/denovoassembler-users >>> >
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