[BioC] shortread base quality

[David martin]

Not really Martin,
It's the score for each nucleotide so the matrix should be something 
like this

	1 2 3 4 5 6 7 .. 30
[1,]	36 36 36 36 36 .. 36 #score for each nucleotide at each position of 
the read.
[2,]	36 36 36 36 36 .. 36
[3,]	36 36 28 36 36 .. 36
[4,]	36 36 36 36 28 .. 36
[5,]	36 28 36 36 36 .. 36

Any idea ?

On 08/24/2012 06:30 PM, Martin Morgan wrote:
> On 08/24/2012 07:09 AM, David martin wrote:
>> Hi,
>> I'm trying to get the quality scores for each nucleotide for each read
>> from the fastq file.
>> Here is how it starts. I know to get average scores for reads but not
>> for each individual nucleotide of each read.
>>
>>
>>
>> file <- "file.fastq"
>> fqfile <- paste(basename(file),"",sep="")
>> path <- dirname(file)
>> sp <- SolexaPath(path,dataPath=path,analysisPath=path)
>> fq <- readFastq(sp, fqfile)
>>
>> #Get quality scores
>> score <- alphabetScore(fq)
>>
>> #Gives the sum of the base quality scores for each read
>> aveScore <- score / width(fq)
>
> try alphabetFrequency, e.g.,
>
>    ragged = narrow(quality(rfq), 1, width=c(20, 30)) ## recycle width
>    alf = alphabetFrequency(ragged)
>
>  > dim(alf)
> [1] 256  94
>  > alf[1:5, 1:5] # not very exciting at this end...
>         ! " # $
> [1,] 0 0 0 0 0
> [2,] 0 0 0 0 0
> [3,] 0 0 0 0 0
> [4,] 0 0 0 0 0
> [5,] 0 0 0 0 0
>
>
> Martin
>
>>
>> #How can i get the score for each base for each read ????
>>
>> thanks,
>>
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>
>