[mira_talk] Re: no singlets on the 454 EST aseembly?

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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