Hi Hao-Ping, Mauve Contig Mover never merges contigs, it only assigns an ordering to contigs for which an ordering can be inferred. If a contig has no sequence identity to the reference genome at all, that contig is not ordered by MCM.
Did you paste the entire scaffold_contigs.tab file in your e-mail? If so, the line suggests that only one contig named "[1,4540734]" was ordered by MCM. Given that contig's name, I'm going to assume that the single scaffold (contig) contains nearly all of the 4.5Mbp genome of your organism, and the remaining 8 scaffolds in your input file are very small. They may not have any recognizable nucleotide-level sequence identity to your reference organism. Hope that helps, -Aaron On Tue, 2009-08-11 at 14:54 -0700, Hao-Ping Chen wrote: > Hi there, > > I currently have 9 scaffolds (about 4.5Mb) in my draft genome and > would like to use Mauve Contigs Mover to order these scaffolds. My > reference sequence (about 7Mb in gbk file) is from a close-related > organism. I put all 9 scaffolds in one fasta file. The content of the > file is as following: > > >Scaffold1 > atttg....... > >Scaffold2 > ttgcggtacc..... > >Scaffold3 > aaattggatc..... > > The output of my "scaffold_contigs.tab" is as following: > > Ordered Contigs > type label contig strand left_end right_end > contig [1,4540734] chromosome forward 1 4540734 > > >From this result, it seems likely that all 9 scaffolds have been > merged into one contig during the run. I can not obtain the > information regarding the scaffold order in genome. Is there anyone > can help me to solve this problem? > > Thanks, > > Hao-Ping > > ------------------------------------------------------------------------------ > Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day > trial. Simplify your report design, integration and deployment - and focus on > what you do best, core application coding. Discover what's new with > Crystal Reports now. http://p.sf.net/sfu/bobj-july > _______________________________________________ > Mauve-users mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/mauve-users ------------------------------------------------------------------------------ Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july _______________________________________________ Mauve-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/mauve-users
