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.
------------------------------------------------------------------------------
_______________________________________________
Mauve-users mailing list
Mauve-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/mauve-users

Reply via email to