On 07/01/14 05:55 PM, Rick White wrote: > Hello Sebastien, > > Do I have to flip the reads (to rev comp)? > http://thegenomefactory.blogspot.ca/2012/09/using-velvet-with-mate-pair-sequences.html
no > > Also, I have merged both Mates + Fragments with overlapping reads with FLASH. > Ray performs better with unmerged paired reads. > Then I did a quick cat command of those into a single file. > Ray supports many input files. > How would my Ray option/command change to include those? > > Cheers and many thanks > Rick > > > On Tue, Jan 7, 2014 at 2:46 PM, Sébastien Boisvert > <sebastien.boisver...@ulaval.ca <mailto:sebastien.boisver...@ulaval.ca>> > wrote: > > On 07/01/14 05:41 PM, Rick White wrote: > > Hello, > > I do. I have a standard fragment library + a long mate pair library. > > How would I make use of them in Ray? What would my options/command be? > > > mpiexec -n 99 Ray -k 31 \ > -p standard_1.fastq.gz standard_2.fastq.gz \ > -p mate_1.fastq.gz mate_2.fastq.gz 20000 2000 \ > > > (You can also try without the manually provided mean and standard > deviation ("20000 2000").) > > Cheers > Rick > > > > On Tue, Jan 7, 2014 at 2:38 PM, Sébastien Boisvert > <sebastien.boisvert.3@ulaval.__ca <mailto:sebastien.boisver...@ulaval.ca> > <mailto:sebastien.boisvert.3@__ulaval.ca > <mailto:sebastien.boisver...@ulaval.ca>>> wrote: > > On 07/01/14 05:01 PM, Rick White wrote: > > > Hello, > > Is there a way to assembly long 20kb mate pair libraries on > Ray? > > > You'll need shorter libraries to complement the 20kb mate pair > library. > > > Both used the MiSeq 250x2 bp technology. > > Cheers > Rick > > > > > > > > > -- > Richard Allen White III M.S. > PhD Candidate - Suttle Lab > Department of Microbiology & Immunology > The University of British Columbia > Vancouver, BC, Canada > cell. 604-440-5150 > http://www.ocgy.ubc.ca/~suttle/ <http://www.ocgy.ubc.ca/%7Esuttle/> > > ------------------------------------------------------------------------------ Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk _______________________________________________ Denovoassembler-users mailing list Denovoassembler-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
