Read my answers below.
nikos ioannidis a écrit : > 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) In your numbers above it is not the case. > > > 2) because i use jumping libraries > should I use them differently in Ray > or process them with a tool? You have to remove adapters unrelated to your sample. > > 3)Generally using jumping libraries > should I handle them differently, or reverse them? I downloaded the EBI data to try it. > 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 ------------------------------------------------------------------------------ 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
