[mira_talk] Re: Mappging to Reference
- From: Saulo Alves <sauloal@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Wed, 28 Jul 2010 16:12:06 +0200
Hello Bastien,
I have used Mira 3.02 with the following parameters
./bin/mira -project=crypto -job=mapping,genome,accurate,solexa
COMMON_SETTINGS -GE:kcim=yes -AS:sd=yes -SK:not=8 SOLEXA_SETTINGS
-LR:ft=fastq -CL:qc=yes -CL:qcmq=25 -GE:tismin=300:tismax=900
Except for the late presence of the rail-reads, is there any mistake in the
assembly I should be aware of?
And, most important, those "deletions" in the regions not covered by any
read, should I trust it once there are so many of them? could it be a
problem in the sequencing instead of the program?
Regards
----------------
s.
On Tue, Jul 27, 2010 at 10:18 PM, Bastien Chevreux <bach@xxxxxxxxxxxx>wrote:
> On Montag 26 Juli 2010 Saulo Alves wrote:
> > Hello Bastien,
> > As you can see there are regions covered exclusively by the rail-reads
> and
> > the reference sequence.
>
>
> Well, clear thing: none of your reads covers the given position in the
> contig.
> The "railreads" you should not see at all, except in intermediate results.
>
> I conclude that you are using some older version of MIRA where I forgot to
> switch off the output of rail reads. Please switch to a newer version,
> 3.0.5
> or 3.2.0rc1 (not rc2, I just discovered a regression there).
>
> Best,
> Bastien
>
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