The N50 value is about contigs>=500.
Another question, I have made a similar question again but I want to be sure I assembled the rhodobacter 2.4.1 with AllpathsLg and Ray -k 31 -p (the following libraries) using the following libraries: as fragment lib: http://www.ebi.ac.uk/ena/data/view/SRX000946 and jumping libs : http://www.ebi.ac.uk/ena/data/view/SRX016062 http://www.ebi.ac.uk/ena/data/view/SRX016063 but I get totally diferrent results for example for Ray: N50 for Contigs >= 100 nt 4.579 N50 for Contigs >= 500 nt 5.611 N50 for Scaffolds >= 100 nt 4.931 N50 for Scaffolds >= 100 nt 5.993 and AllPathsLg N50 contigs 240.400 N50 scaffolds 2.956.000 1) isn't it strange that the N50 for Contigs >= 100 nt is bigger than N50 for Contigs >= 500 nt ? (The same for scaffolds) 2) because i use jumping libraries should I use them differently in Ray or process them with a tool? 3)Generally using jumping libraries should I handle them differently, or reverse them? Thank you. On Mon, Jun 4, 2012 at 5:28 PM, nikos ioannidis <niioa...@gmail.com> wrote: > > Hello, > > > i want to ask if i run twice the Ray is it normal to take slightly different > results? > Also when i use more cpus the time shouldn't reduce? or depents? > And another one, when i use more cpus this affects my results? > for example using 224 cpus for e.coli i get N50=80011 > and if i use 64 cpus i get N50=68137, is normal to have a value +- 10K?? > > > Thank you. > ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ Denovoassembler-users mailing list Denovoassembler-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
