On Wed, Feb 23, 2011 at 1:17 PM, Tony Travis <a.travis@xxxxxxxxxx> wrote: > > Hi, Bastien. > > I'm assembling Solexa paired-end reads with MIRA using the default Solexa > read-naming convention, but I have no idea if MIRA is actually using the > mate-pair information. I've looked at the logs, but I can't find any > information about mate-pairs. > > I have to admit that I just assumed mate-pair information is used by MIRA. > However, when I used the "tablet" viewer to examine a MIRA 'ace' file from > my Solexa paired-end assembly, it showed no mate-pairs. Hi Tony, Ace files don't store paired end information explicitly, so Tablet can't show you anything. I therefore wrote a MIRA assembly format (MAF) to SAM converter which should then allow you to see the pairs in Tablet (or any other SAM/BAM viewer): https://github.com/peterjc/maf2sam I'm happy to have any feedback on the MIRA list. Peter -- You have received this mail because you are subscribed to the mira_talk mailing list. For information on how to subscribe or unsubscribe, please visit http://www.chevreux.org/mira_mailinglists.html