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: [email protected]
> To: [email protected]
> CC: [email protected]; [email protected];
[email protected]
> 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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