On 17 février 2014 10:08, jjv5.j...@gmail.com [jjv5.j...@gmail.com] de la part de James Vincent [james.vinc...@uvm.edu] wrote: > À : Sébastien Boisvert > Cc : denovoassembler-users@lists.sourceforge.net > Objet : Re: RE : [Denovoassembler-users] How to determine unassigned reads or > contigs in Ray communities > > Thanks for the information. > > I see a discrepancy in counts though. The file > BiologicalAbundances/_DeNovoAssembly/Contigs.tsv contains only 38 > contigs that have non-zero colored k-mers. In the taxonomy profiles > produced from these contigs at the species level: > 0.Profile.TaxonomyRank=species.tsv > > there are 575 species present with some proportion. This does not seem > right. Any clue where I might have gone wrong?
The proportions are based on k-mer matches and not assembled sequences. Does that explain it ? > > Thanks, > Jim > > On Mon, Feb 17, 2014 at 9:56 AM, Sébastien Boisvert > <sebastien.boisver...@ulaval.ca> wrote: >> >> On 13 février 2014 14:58, jjv5 [j...@jjv5.net] wrote: >>> À : denovoassembler-users@lists.sourceforge.net >>> Objet : [Denovoassembler-users] How to determine unassigned reads or >>> contigs in Ray communities >>> >>> Hello, >>> >>> Before I try a few things myself I thought I might ask if there is a >>> way to collect either final assembled contigs that were not assigned >>> any taxonomy (under BiologicalAbundances)? >>> >>> I think I could collect the contig IDs of everything that was >>> assigned, but since they occur at many different levels (species to >>> kingdom) this seems messy and error prone. Do unassigned contigs >>> already show up somewhere else? >> >> >> You can use Assembly/BiologicalAbundances/_DeNovoAssembly/Contigs.tsv. >> >> The column "Colored k-mers" tells how many k-mers in the contig are colored. >> 0 means that the >> contig is unassigned. >> >>> >>> On a related note, is there a way to find individual reads that were >>> not included in any contigs? >> >> No, I am afraid. And I never got the time to implement that as of late. >> >> >>> >>> Thanks, >>> Jim >>> >>> ------------------------------------------------------------------------------ >>> Android apps run on BlackBerry 10 >>> Introducing the new BlackBerry 10.2.1 Runtime for Android apps. >>> Now with support for Jelly Bean, Bluetooth, Mapview and more. >>> Get your Android app in front of a whole new audience. Start now. >>> http://pubads.g.doubleclick.net/gampad/clk?id=124407151&iu=/4140/ostg.clktrk >>> _______________________________________________ >>> Denovoassembler-users mailing list >>> Denovoassembler-users@lists.sourceforge.net >>> https://lists.sourceforge.net/lists/listinfo/denovoassembler-users ------------------------------------------------------------------------------ Android apps run on BlackBerry 10 Introducing the new BlackBerry 10.2.1 Runtime for Android apps. Now with support for Jelly Bean, Bluetooth, Mapview and more. Get your Android app in front of a whole new audience. Start now. http://pubads.g.doubleclick.net/gampad/clk?id=124407151&iu=/4140/ostg.clktrk _______________________________________________ Denovoassembler-users mailing list Denovoassembler-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
