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. ________________________________________ 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
