Hi Nikos. On 10 July 2012 12:53, nikos ioannidis <niioa...@gmail.com> wrote: > Hello, > > is correct that the total scaffolds length should be smaller than the > genomic size of a genome?
That depends. How correct are the size of your genome? If it's E. coli, then the scaffolds should be the same or probably a bit shorter, but if it's an species from the wild where the estimate of the genome size is from flowcytometri or similar, e. g. you know the genome should be around 110 Mbp, then your assembly might be a more accurate estimate of the genome size. > between 2 assembly tries, with same N50 of Scaffolds and same number > of scaffolds, > which considered better the one woth igger total scaffold length than > the genomic size or the one with > approximately lower or equal with the genomic size? If it's much larger, then it might be a misassembly. If your genome size estimate is correct (4,639,221 bp for E. coli K-12 for example), and your scaffold sum up to 4.9 Mbp for the same species, then I would chose the shorter one. Ole > > > 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
