
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. 
 
> 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@fhcrc.org
> To: fuad_gwadry@hotmail.com
> CC: bioc-sig-sequencing@r-project.org; apratap@som.umaryland.edu; johannes.waage@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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