Hi Jingjing, Anna Rissman (who authored the contig mover) can give the definitive answer, but my understanding is that such contigs are labeled as being conflicted. In cases where the contig aligns to one chromosome (or region of a chromosome) over a much greater length than the other region, it will be anchored in that region.
Best, -Aaron On Mon, 2013-08-12 at 10:14 +0000, Jingjing Jin wrote: > Dear all, > > I am interested about the contig order function of Mauve. > > > However, I am a little confuse about it how to deal with this case: > > If one part of contig align to one chromosome from reference genome, > another part of a contig align to another chromosome from reference > genome. > > How will Mauve deal with this case and order them? > > Thanks! > > Jingjing -- Aaron E. Darling, Ph.D. Associate Professor, ithree institute University of Technology Sydney Australia http://darlinglab.org twitter: @koadman UTS CRICOS Provider Code: 00099F DISCLAIMER: This email message and any accompanying attachments may contain confidential information. If you are not the intended recipient, do not read, use, disseminate, distribute or copy this message or attachments. If you have received this message in error, please notify the sender immediately and delete this message. Any views expressed in this message are those of the individual sender, except where the sender expressly, and with authority, states them to be the views of the University of Technology Sydney. Before opening any attachments, please check them for viruses and defects. Think. Green. Do. Please consider the environment before printing this email. ------------------------------------------------------------------------------ Introducing Performance Central, a new site from SourceForge and AppDynamics. Performance Central is your source for news, insights, analysis and resources for efficient Application Performance Management. Visit us today! http://pubads.g.doubleclick.net/gampad/clk?id=48897511&iu=/4140/ostg.clktrk _______________________________________________ Mauve-users mailing list Mauve-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mauve-users
