[mira_talk] Re: no singlets on the 454 EST aseembly?
- From: Zhao Lai <zhaolai2008@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Tue, 25 Jan 2011 14:00:43 -0500
Dear Bastien,
Thanks for the quick response. Actually I'm waiting for your reply to
conform one assembly to proceed forward. So my question is: do I have to
perform the MIRA assembly again by changing the parameters or actually the
singlets information is somewhere in the output folder and I can just go to
grab them in the previous assembly folder?
Thanks
Zhao
On Tue, Jan 25, 2011 at 1:37 PM, Bastien Chevreux <bach@xxxxxxxxxxxx> wrote:
> On Tuesday 25 January 2011 16:59:40 Zhao Lai wrote:
> > We have been using MIRA for 454 transcriptome sequences assembly for a
> > while. This is the first time we use the new version (version3.2.1) to
> > assembly one full plate of 454 titanium normalized EST data.
> Surprisingly,
> > there is no singlet in the output! Everything has been assembled to
> contig.
> >
> > The command we used for the 454 EST assembly: /nfs/bio/sw/bin/mira
> > -project=ISI -fasta -job=denovo,est,accurate,454 -noclipping -notraceinfo
> > 454_SETTINGS -AS:mrl=50 -AL:mrs=94 -OUT:sssip=yes -CL:bsqc=yes. I checked
> > the manual and saw this part: "-OUT:sssip=yes" which I assume this should
> > send all singlets to the results, and it's the same command I used before
> > for other EST 454 sequencing assembly project with the old version . So I
> > can not explain why there is no singlets for this assembling. Don't know
> > whether the new version is the reason.
>
> From the manual under
>
> http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html#sect_ref_output_out
>
>
> [savesimplesingletsinproject(sssip)=on|yes|1,off|no|0]
>
> Default is no. Controls whether 'unimportant' singlets are written to
> the result files.
> [Note] Note
> Note that a value larger 1 of the [-AS:mrpc] parameter will disable the
> function of this parameter.
>
> -AS:mrpc is set to values larger than 1 for most default assembly types
> (the output log should tell you that also when in doubt for your special
> parameter
> combination).
>
> Does this help you?
>
> B.
>
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