> Hi, > >>However I am not convinced that this will produce an good assembly... > >>I have seen better peaks in my life. ;) > > Yeah, that's why I just quit the job after looking at the distribution. > > I've decided to go with a trimming method that just chops everything off > below Q=30. This will leave me with number of very short reads, but also > keep many full > length reads that are of very good quality.
You peak will be more explicit with less sequencing errors so filtering below Q=30 is a good idea for your data. > I'm reluctant those short reads out however, because it would muddle the > paired end ordering, and it appears that it would be a fair amount of work > and somewhat of a waste to > also throw out the other pair that might be a > reasonable enough read. But, how would Ray deal with reads that might be > below the Kmer length? Would this cause a problem? > > Walter They will be skipped. Sébastien ------------------------------------------------------------------------------ 5 Ways to Improve & Secure Unified Communications Unified Communications promises greater efficiencies for business. UC can improve internal communications as well as offer faster, more efficient ways to interact with customers and streamline customer service. Learn more! http://www.accelacomm.com/jaw/sfnl/114/51426253/ _______________________________________________ Denovoassembler-users mailing list Denovoassembler-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/denovoassembler-users