[mira_talk] Re: Using mira - first impression
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Mon, 24 Aug 2009 22:34:04 +0200
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
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