Sebastien: Here are my attempted replies. [I CC'ed the mailing list as this is Ray-related.]
On 12/03/2012 11:33 AM, Forster, Robert wrote: > Hi Sebastien: > >> I've been investigating using Ray for my metagenomic samples >> (discussed this on the list a few months ago). I've used Ray rc 2.08 >You mean Ray 2.0.0-rc8 ? Yes >>on four samples of HiSeq data(one lane each sample/treatment) and I end >>up reducing the dataset, but still have 3.5 million or so contigs in each >>sample (N50 143,contigs > 500 89,700 N50 1137, largest 37kb). >What k-mer length are you using ? At this point just the default (21?). However I recompiled ray-v2.1.0 to use up to 64 yesterday. I thought I would test different kmer lengths (31-45?) >How many reads per sample do you have ? each sample has about 72.5 million >PE reads after basic QC (so 145 million) plus I have some 454 single end reads >I could throw in. >Did you run Ray with paired reads ? Yes >> I am in the stages of convincing my Centre to purchase a MiSeq, so I >>can get 2x250 reads as well, hoping this will help. >How are you preparing your DNA libraries ? This is in the future, but >probably Nextera to begin. >What's the insert size ? Not yet determined, but with it may be Nextera quite >variable (300-1600?) >With de Bruijn graph assemblers, what's important to get through repeats is >mostly good insert sizes. > If not, I will contract this out in January. I do have some single >read 454 data as well. > > The experiment is a unique one, using the rumen of MuskOxen fed straw >to look for biomass degrading enzymes. We published a metatranscriptome >paper in PLoS One about the rumen fungal enzymes, but I'd like to get a better >handle on the metagenome sequencing I've done. > Sure. >> I found a talk on-line that you did at Argonne about metagenome >>assembly. So I'm curious about Ray Meta. Is it possible to test it out as >>compared to the standard Ray? > >Ray Meta is a workflow with Ray. The heuristics of Ray 2.0.0-rc8 are those of >Ray Meta. OK so I don't need to use any options to enable it. Would I be better off trying a version from github? I'd need to work out how to do that. >Our paper describing Ray Meta was accepted for publication in the journal >Genome Biology. >It should appear soon on the publisher website. Looking forward to seeing it! >> Also, once I get new the MiSeq reads (another possible 15 GB per >>sample) the assembly may be beyond our capacity here in Lethbridge. I was >>wondering whether you may be interested in a collaboration to analyse the >>data? Yes. That would be interesting. ------------------------------------------------------------------------------ Keep yourself connected to Go Parallel: BUILD Helping you discover the best ways to construct your parallel projects. http://goparallel.sourceforge.net _______________________________________________ Denovoassembler-users mailing list Denovoassembler-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
