[mira_talk] Re: awkward letters in assembled data

  • From: Arun Rawat <rawat_arun@xxxxxxxxx>
  • To: "mira_talk@xxxxxxxxxxxxx" <mira_talk@xxxxxxxxxxxxx>
  • Date: Thu, 29 Sep 2011 11:58:25 -0700 (PDT)

For vector removal i tried several things, NCBI Univec, etc..

What about 454 adapters?


________________________________
From: Visam Gültekin <teutara@xxxxxxxxxxx>
To: Mira Talk <mira_talk@xxxxxxxxxxxxx>
Sent: Thursday, September 29, 2011 11:49 AM
Subject: [mira_talk] Re: awkward letters in assembled data


 

That is right, there is no .qual file. For vector removal i tried several 
things, NCBI Univec, etc..
It seems different preprocessing steps outputs -more or less-  same results. 
For that reason i am almost confident that the reads i have are clean, but 
still no .qual file.


mira --project=run4 --job=est,accurate,denovo,454 -notraceinfo 
>454_SETTINGS -AS:epoq=no -CL:qc=no:cpat=no 
>-AL:egp=no -LR:wqf=no:lsd=1:ft=fasta -CO:fnicpst
>
will be my best shot i guess?

V.G.


> Subject: [mira_talk] Re: awkward letters in assembled data
> From: bach@xxxxxxxxxxxx
> Date: Thu, 29 Sep 2011 20:44:03 +0200
> To: mira_talk@xxxxxxxxxxxxx
> 
> On Sep 29, 2011, at 20:39 , Peter Cock wrote:
> > That suggests you have FASTA sequences (are there
> > matching QUAL files with quality scores?).
> 
> I have the bad feeling that there are no qualities.
> 
> Vi
 sam, in that case you *do* want to read about assembly without qualities.
> 
> B.
> 
> 
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