Hi Ariadna, On Tue, 2010-04-27 at 12:18 +0200, Ariadna Rodriguez Chamorro wrote: > Dear All, > I need the LCB boundary output file which mauve_user_guide(v 2.3.1) > said is a "file that complements the permutation matrix file with > information about the LCB boundaries". I thought it was possible to > obtain it by exporting the "permutations" but apparently that's not > enough 'cause I only got the .permutations file and not the LCB > boundaries one. > I will appreciate very much if anyone can give me a hint to output > this file, I've been looking once and other time through the docs but > I can't understand what's the missing point. >
The LCB boundary file can be created via command-line tools, but not yet through the graphical interface. Sorry for any confusion. Instructions for generating the LCB boundary file from a progressiveMauve alignment can be found in step 2 of the instructions on this page: http://bioinformatics.org.au/barphlye Two programs are required: projectAndStrip, and makeBadgerMatrix. Both are available for Mac, Windows, and Linux from the "other programs" link in the "Successful builds" section of this web page: http://gel.ahabs.wisc.edu/mauve/snapshots/ If you're using linux or mac, don't forget to make the projectAndStrip and makeBadgerMatrix programs executable before trying to run them; it can be done with: chmod 755 projectAndStrip chmod 755 makeBadgerMatrix Also, beware that those programs assume the input genomes are a single chromosome. Multiple chromosomes/contigs/plasmids will be concatenated together, which may not be a desirable result depending on what you're trying to do... Hope that helps, -Aaron ------------------------------------------------------------------------------ _______________________________________________ Mauve-users mailing list Mauve-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mauve-users
