Re: phrap contig , apply contig quality values?

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Re: phrap contig , apply contig quality values?

Phillip SanMiguel
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.

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