On 06/12/13 03:50 PM, Hornung, Bastian wrote: > I have only one 454 dataset here, but when I put that together with my > Illumina data, I got worse assemblies with it. I assumed, like Sebastian > mentioned, that this could be due to the homopolymer errors.
I would say it depends on the Illumina-to-454 ratio too. Ray is sensitive to reproducible sequencing errors, like those homopolymers found in 454 reads and also in Ion Torrent reads. > ________________________________________ > From: raw...@gmail.com [raw...@gmail.com] > Sent: Friday, December 06, 2013 7:20 PM > To: Sébastien Boisvert > Cc: denovoassembler-users@lists.sourceforge.net; Sébastien Boisvert > Subject: Re: [Denovoassembler-users] Ion Torrent + Illumina Hybrid Assembly > on Ray > > Hello, > > Yes, I tried both. When I put Ion torrent reads with illumina or do just Ion > torrent reads I get terrible assemblies. I am more of a fan of illumina but I > have the Ion Torrent data and would like to get something out of it. > Also, any thoughts for 454 and Illumina Hybrid assembly? I get okay > assemblies but it wondering if there were ways to improve them. > > Cheers > Rick > ------Original Message------ > From: Sébastien Boisvert > To: Rick White > Cc: denovoassembler-users@lists.sourceforge.net > Cc: Sébastien Boisvert > Cc: Pier-Luc Plante > Subject: Re: Ion Torrent + Illumina Hybrid Assembly on Ray > Sent: Dec 6, 2013 9:09 AM > > On 26/11/13 02:22 PM, Rick White wrote: >> I have some 200bp Ion Torrent Mate Pair data, Paired 250x2 MiSeq reads and >> have merged the overlapping reads from the Illumina data. >> >> When I try to run standard parameters in Ray the assemblies are worse with >> the addition of the Ion Data. >> >> Do you have parameters that could help me out? >> > > I don't. > > > It may be due to homopolymers. > > > By the way, Ray will perform better with unmerged paired reads. Did you try > unmerged paired Illumina reads too ? > >> 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/> >> >> > > > Sent from my “contract free” BlackBerry® smartphone on the WIND network. > ------------------------------------------------------------------------------ > Sponsored by Intel(R) XDK > Develop, test and display web and hybrid apps with a single code base. > Download it for free now! > http://pubads.g.doubleclick.net/gampad/clk?id=111408631&iu=/4140/ostg.clktrk > _______________________________________________ > Denovoassembler-users mailing list > Denovoassembler-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/denovoassembler-users > > > > ------------------------------------------------------------------------------ > Sponsored by Intel(R) XDK > Develop, test and display web and hybrid apps with a single code base. > Download it for free now! > http://pubads.g.doubleclick.net/gampad/clk?id=111408631&iu=/4140/ostg.clktrk > _______________________________________________ > Denovoassembler-users mailing list > Denovoassembler-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/denovoassembler-users > ------------------------------------------------------------------------------ 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
