Hi Diego, On Wed, 2013-07-10 at 16:43 +0200, [email protected] wrote: > BUT I would need get a file with the position of the LCBs on each > genome, that is, the start and end position of each LCB refered to each > scaffold of each genome. > Actually, that information that I need, is shown in the graphical > interface, in the bottom-left of the window when you move the cursor > through each genome.
Just to clarify, it sounds like you're asking for the scaffold-local coordinates of the LCBs, rather than the coordinates stored in the mauve XMFA, which represent a concatenation of all scaffolds in each input genome. If that's indeed what you're asking for, there's no direct way to generate a list of these scaffold local coordinates as such. One indirect approach might be to use the xmfa2maf program and extract the coordinates from the resulting MAF file. In the MAF format the coordinates of all aligned regions are recorded in scaffold-local coordinate systems. xmfa2maf can be obtained from the "other programs" links on the mauve snapshots website. Hope that helps. -Aaron -- 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. ------------------------------------------------------------------------------ See everything from the browser to the database with AppDynamics Get end-to-end visibility with application monitoring from AppDynamics Isolate bottlenecks and diagnose root cause in seconds. Start your free trial of AppDynamics Pro today! http://pubads.g.doubleclick.net/gampad/clk?id=48808831&iu=/4140/ostg.clktrk _______________________________________________ Mauve-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/mauve-users
