Hello, I am using Mauve as part of the ClonalFrame pipeline for bacterial genomes. I am very excited about what I can do with these tools, but I'm hitting a snag with the stripSubsetsLCBs program (recently downloaded from the "successful builds" webpage)
My understanding is that this program should trim the alignment file down just the core region (i.e. shared by all genomes). However, I have noticed that many of the blocks in the alignment file have large indels in them (>1 kb). I ran Mauve with the default settings, and my understanding is that gaps larger than 20bp would not be included in the core region. At it's worst, I have a block that is >5kb, but only about 300 bp are aligned across all genomes. I did a sliding-window analysis of a bunch of the blocks, and I think I see what's going on. These large gaps always seem to be at the end of the block. For example, my original alignment file had one large block with gaps at each end, and two internal regions with indels. This was split into three blocks (removing the internal gaps) and the gap at the front was removed. The gap at the back was NOT removed. Is this expected behavior? If not, is there anything I can do to fix this? Thanks, Adam UC Berkeley ------------------------------------------------------------------------------ Don't let slow site performance ruin your business. Deploy New Relic APM Deploy New Relic app performance management and know exactly what is happening inside your Ruby, Python, PHP, Java, and .NET app Try New Relic at no cost today and get our sweet Data Nerd shirt too! http://p.sf.net/sfu/newrelic-dev2dev _______________________________________________ Mauve-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/mauve-users
