What do you see in LibraryStatistics.txt ? This file contains auto-calibrated insert size by Ray.
On 12/03/2012 02:42 PM, Forster, Robert wrote: > 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. > > ------------------------------------------------------------------------------ LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial Remotely access PCs and mobile devices and provide instant support Improve your efficiency, and focus on delivering more value-add services Discover what IT Professionals Know. Rescue delivers http://p.sf.net/sfu/logmein_12329d2d _______________________________________________ Denovoassembler-users mailing list Denovoassembler-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
