[Bioc-sig-seq] alignQuality

[Martin Morgan]

Fuad Gwadry wrote:
> Hi Martin
>  
> Thank-you for your help with readAligned. The quality scores are in the 
> correct range now.
>  
> Going back to my question on alignQuality I had a couple of days ago I 
> found found that all of the values are NAs. They exist since I am still 
> able to generate the quality scores matrix. I typed ?alignQuality and it 
> doesn't appear I'm missing any parameters.

There are two types of 'qualities' possible.

One is of the quality of the base calls, and these are quality(aln).

The other is the quality of the alignment, which is retrieved by 
alignQuailty(aln).

Bowtie does not output alignment qualities. Hence, alignQuality(aln) 
returns all NA.

Martin

>  
>  > alignQuality(aln)
> class: NumericQuality
> quality: NA NA ... NA NA (4933275 total)
> q <- quality(alignQuality(aln))
>  > sum(is.na(q))
> [1] 4933275
> 
>   
>  > Date: Wed, 5 Aug 2009 09:21:56 -0700
>  > From: mtmorgan at fhcrc.org
>  > To: fuad_gwadry at hotmail.com
>  > CC: bioc-sig-sequencing at r-project.org; apratap at som.umaryland.edu; 
> johannes.waage at gmail.com
>  > Subject: Re: [Bioc-sig-seq] Problem with ShortRead reading quality 
> scores from bowtie
>  >
>  > Hi Faud --
>  >
>  > > get NAs in both cases. Let me know how I can help to trouble shoot 
> this.
>  >
>  > NA's in alignQuality are present when the reads did not align; not all
>  > of the values will be NA. see below for the issue with base quality 
> scores.
> 
> Fuad
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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