Hi Mariam, Perhaps the easiest way to do this is via the graphical interface. If you load the final alignment generated by the contig mover in the Mauve viewer, any unplaced contigs will appear on the right side of the draft genome track. They will be unaligned, and therefore will not have any similarity plot or connecting lines to the reference genome. If you hover the mouse over one of those contigs its name will appear in the lower right corner of the window. If you need an automated approach you might be able to base it off of the _contigs.tab file in the output directory, which describes what was done with each contig at each reorder iteration.
Best, -Aaron On Fri, 2014-05-23 at 09:30 -0500, Mariam Iskander wrote: > Hello, > > I am using MCM to order some contigs, and I would like to exclude the > contigs with no ordering information associated with them. According > to the User Guide, the contigs with no LCBs are included at the end of > the genome, but I could not figure out where the ordered contigs end > and the unordered ones begin. I looked through the output files and I > couldn't find this information. Is it possible to get the list of > contigs with no LCBs? > > Thank you very much. > > Mariam > > ------------------------------------------------------------------------------ > "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE > Instantly run your Selenium tests across 300+ browser/OS combos. > Get unparalleled scalability from the best Selenium testing platform available > Simple to use. Nothing to install. Get started now for free." > http://p.sf.net/sfu/SauceLabs > _______________________________________________ > Mauve-users mailing list > Mauve-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/mauve-users -- 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. ------------------------------------------------------------------------------ The best possible search technologies are now affordable for all companies. Download your FREE open source Enterprise Search Engine today! Our experts will assist you in its installation for $59/mo, no commitment. Test it for FREE on our Cloud platform anytime! http://pubads.g.doubleclick.net/gampad/clk?id=145328191&iu=/4140/ostg.clktrk _______________________________________________ Mauve-users mailing list Mauve-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mauve-users
