From aumanga from biggjapan.com  Wed Feb 25 01:45:51 2009
From: aumanga from biggjapan.com (Umanga)
Date: Wed Feb 25 07:15:59 2009
Subject: [Automated-sequencing] phrap contig ,apply contig quality values?
Message-ID: <22197180.post@talk.nabble.com>


Greetings all,
Firstof all, come from Computer science background ,so I have very little
knowledge in Bioinformatics.
Now  my question ;
I assemble AB1 files using phred/phrap.I noticed that after assembling using
'phrap', it generates contig file (say 'seq.contigs') and a contig-quality
file ('seq.contigs.qual').

Now,I want to get the same contig which generated by ChromasPro using phrap.

I noticed that ,if I ignore the config bases with quality value '0' (which
stored in seq.contigs.qual) , I can get almost same sequence as ChromasPro.
Is this correct?
This there a parameter to do this in 'phrap' itself? 

Thanks in advance,
Umanga
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From pmiguel from purdue.edu  Wed Feb 25 07:37:05 2009
From: pmiguel from purdue.edu (Phillip San Miguel)
Date: Wed Feb 25 07:38:55 2009
Subject: [Automated-sequencing] phrap contig , apply contig quality values?
In-Reply-To: <mailman.320.1235564159.13724.autoseq@net.bio.net>
References: <mailman.320.1235564159.13724.autoseq@net.bio.net>
Message-ID: <49A53B71.90709@purdue.edu>

Umanga wrote:
> Greetings all,
> Firstof all, come from Computer science background ,so I have very little
> knowledge in Bioinformatics.
> Now  my question ;
> I assemble AB1 files using phred/phrap.I noticed that after assembling using
> 'phrap', it generates contig file (say 'seq.contigs') and a contig-quality
> file ('seq.contigs.qual').
> 
> Now,I want to get the same contig which generated by ChromasPro using phrap.
> 
> I noticed that ,if I ignore the config bases with quality value '0' (which
> stored in seq.contigs.qual) , I can get almost same sequence as ChromasPro.
> Is this correct?
> This there a parameter to do this in 'phrap' itself? 
> 
> Thanks in advance,
> Umanga

Hi Umanga,
	Yes, you should remove the bases with zero quality values from the ends 
of phrap contigs. A quality value of zero indicates the base call is 
random noise. I usually trim the ends of contigs back until I hit the 
first base with a 20 or higher quality value.
	I don't know of a method to force phrap to do this. It would be nice.
	I've never used Chromas or ChromasPro. But different assembly engines 
may produce different contigs from the same data set.
Phillip