[mira_talk] Re: singlets fasta file..

  • From: Visam Gültekin <teutara@xxxxxxxxxxx>
  • To: Mira Talk <mira_talk@xxxxxxxxxxxxx>
  • Date: Wed, 23 Mar 2011 21:24:47 +0000

Dear Mr.Chevreux,
Thank you for your reply, although i try to set the -AS:mrpc=1 , i do get 
"unrecognized string or unexpected character", it is because of parsing 
parameters i guess, but i can not see the problem.. what to do?
Visam

From: bach@xxxxxxxxxxxx
To: mira_talk@xxxxxxxxxxxxx
Subject: [mira_talk] Re: singlets fasta file..
Date: Mon, 21 Mar 2011 20:22:16 +0100





On Monday 21 March 2011 11:21:06 Visam Gültekin wrote:
> In some earlier posts, getting singlets as fasta file had been discussed.

MIRA does never output a separate FASTA file with singlets. It however may add 
singlets to regular result FASTA files.

> Although i followed the recommendation, i can see no fasta file for
> singlets.Hhere is the command i used.. mira -project=project_p_run4 -fasta
> -job=denovo,genome,accurate,454 -highlyrepetitive -GE:not=8 -AS:sep=1
> -SK:not=8 -SK:bph=18 -SK:mchr=4096 454_SETTINGS -ED:ace=1 -OUT:sssip=on
> -OUT:stsip=on so i can not see any information about singlets, else of txt
> files. i guess i miss a big notch

Yep. You may or may not have missed the following note in the description of 
the -OUT:sssip and -OUT:stsip parameters:





  Note


  Note that a value larger 1 of the [-AS:mrpc] parameter will disable the
  function of this parameter. 

(see 
http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html#sect_ref_output_out)

As the command line you use takes the default parameter for -AS:mrpc (look at 
the MIRA output log in the top section where all used parameters are listed), 
MIRA won't write singlets to the result files.

Simply set -AS:mrpc accordingly.

B.

PS: trust me: in a 454 genome denovo assembly, you do not want to have 
singklets in your regular results. You have been warned :-)                     
                   

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