[mira_talk] Re: mira 3.9 manifest file for hybrid assembly
- From: Marcelo Brandão <brandao.marcelo@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Fri, 12 Oct 2012 14:21:11 -0600
> Hello guys.
> I am trying to use Mira 3.9.4 to map solexa reads over a 454 contigs. I am
> wouod like to see if this can speedup my results. But, I am having problems
> with the manifest file. Here is the mira 3.4 command line that I would like
> to use:
> mira --project=Mira_SBW_Map3 -job=mapping,genome,accurate,solexa
> -SB:bft=caf -GE:not=15 -SK:mmhr=1:pr=70:hss=2 COMMON_SETTINGS -AS:sd=1
> -DI:trt=/state/partition1/mira SOLEXA_SETTINGS -CL:qc=yes:qcmq=5:qcwl=5
>
> I try this manifest:
> #manifest file for testing mira 3.9
> project = Mira_SBW_Map3
> job = mapping,genome,accurate,solexa
> parameters = -GE:not=15
>
>
>
> readgroup = 454assembly
> technology=454
> data = Mira_SBW_Map3_backbone_in.caf
> as_reference
> parameters = -SB:bft=caf
> -SK:mnr=1:pr=70:hss=2
> -AS:sd=1
> COMMON_SETTINGS -DI:trt=/state/partition1/mira
>
> readgroup = solexareads
> technology=solexa
> data = Mira_SBW_Map3_in.solexa.fastq
> parameters = -AS:sd=1
> SOLEXA_SETTINGS -CL:qc=yes:qcmq=5:qcwl=5
> COMMON_SETTINGS -DI:trt=/state/partition1/mira
>
> But I only get errors.
>
> Can someone help me to wirte a manifest for hybrid assembly?
>
> Really thanks in advance!!
>
>
> Marcelo
>
--
Marcelo Mendes Brandão
Academic Visitor at University of Alberta @ Edmonton
Website: http://bioinfo.esalq.usp.br
AtPIN: http://bioinfo.esalq.usp.br/atpin
SKYPE: mmbrand
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