[mira_talk] Re: mapping
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Tue, 14 Apr 2009 23:53:56 +0200
On Tuesday 14 April 2009 Giuseppe D'Auria wrote:
> Dear all, I noticed in my last mapping assembly that there are "things"
> assembled on my backbone genome where the name is something progressive
> ####1#### to ###nnnn###. The nucleotides are in lowercase and are
> immediately below the backbone. Always perfectly overlap the backbone.
> The strange thing is that sometimes overlap my reads sometimes not. I am
> quite sure they do not belong to my reads
> Somebody know what they are?
Yes. You shouldn't be seeing them at all ... or did you look at some
intermediate files from the log directory? If they're in the final results,
it's
a bug.
These reads are "rail reads" (or "rails"), i.e., reads that MIRA creates
internally during mapping assemblies to guide and speed up assembly. They also
allow nifty things like almost perfect read distribution across different
repeat sites.
Depending on your "--job", MIRA will use certain presets ... but these may not
be ideal for Titanium reads or the newer Solexa 76mers. In case you need to
tweak them: the parameters for these are in the -SB section. Basically, choose
twice the size of your largest reads as length (-SB:brl) and the length as
overlap (-SB:bro). If using technologies with different lengths, take the
longer. E.g. for 454 FLX (assuming an average length of 250 bases) and Solexa
76 mers: -SB:brl=500:bro=250
Regards,
Bastien
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