On Mittwoch 19 August 2009 Martin A. Hansen wrote: > Do these settings look sane? I never figured how to name the Solexa reads > "prep2" - if that is needed. See docs on -SB:lsd and the files in "bbdemo2" to see this in action. A key- value file which looks like this: readname strainname readname strainname readname strainname readname strainname readname strainname ... > And two features I encountered: > 1. bsn is not backbone_strain_name - that long name raises an error. backbone_strainname. My bad. > 2. msr is not documented - and what is the long name of this switch? My bad. merge_short_reads (msr) = {on$|$yes$|$1, off$|$no$|$0}] Default is \underline{yes} for all Solexas when in a mapping assembly, else it's \underline{no}. Can only be used in mapping assemblies. If set to \underline{yes}, \Prog{mira} will merge all perfectly mapping Solexa reads into longer reads while keeping quality and coverage information intact. This features hugely reduces the number of Solexa reads and makes assembly results with Solexa data small enough to be handled by current finishing programs (gap4, consed, others) on normal workstations). All of the above fixed in docs for next release. Regards, Bastien -- 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