Exactly !
> ________________________________________ > De : Adrian Platts [[email protected]] > Date d'envoi : 20 juillet 2011 12:53 > À : Sébastien Boisvert > Cc : Walter Eckalbar; [email protected] > Objet : Re: [Denovoassembler-users] RE : RE : Ray assembly kmer coverage > question > >> >> That is the first thing you should do I think. k=21 will pick up more >> redundant k-mers than k=31 or k=61. >> >> Basically, this is why: >> >> >> If the sequencing error rate is > 4.7% (1/21), then mostly all k-mers will >> be unique and bad for k=21. >> If the sequencing error rate is > 3.2% (1/31), then mostly all k-mers will >> be unique and bad for k=31. >> If the sequencing error rate is > 1.6% (1/61), then mostly all k-mers will >> be unique and bad for k=61. >> >> I believe Illumina HiSeq TruSeq sequencing error rate varies between 0 and 2 >> %. You mileage may vary however depending on the quality of DNA and library >> preparation (nicks >> in DNA for instance during the library preparation). >> > > I believe that most people using long Kmers in assembly have been 3' > trimming/rejecting reads where they fall below (at least) Q=31 on a per read > basis and > with the newer Illumina chemistries at Q=35. I don't know of anyone who is > really putting raw FASTA read data directly into the assemblers - certainly > not when using long Kmers > for exactly the reason above. > > I suppose FASTQ data perhaps but the way the FASTQ data is dealt with can be > pretty different between assemblers so it can have mixed results I think. > > Adrian > > Sébastien ------------------------------------------------------------------------------ 10 Tips for Better Web Security Learn 10 ways to better secure your business today. Topics covered include: Web security, SSL, hacker attacks & Denial of Service (DoS), private keys, security Microsoft Exchange, secure Instant Messaging, and much more. http://www.accelacomm.com/jaw/sfnl/114/51426210/ _______________________________________________ Denovoassembler-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
