Hi Rajeh, On Mon, 2015-11-16 at 17:55 -0600, Ahmad Rajeh wrote: > Hello Mauve-users, > > I have 2 questions: First, could someone please explain seed weight > and minimum LCB to me? The manual's descriptions are unclear to me. > For example, all I want is to consider contigs that share at least 1 > kb with the reference, with maximum 0.01% mismatch. How can I do that?
There is no way to directly apply such filters using the aligner. You would have to write a script that reads the alignments. > > Second, I'd like to extract contigs with breakpoints, i.e. those that > mapped to different regions on the reference. In other words, contigs > that include more than one color. How can I do that? I thought the > _contigs.tabs file would be helpful, but I couldn't find information > about contigs with multiple alignments. I'm afraid generating such a list is another feature that would require some scripting, or further development of the contig mover's java code. -- 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.
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