[BioC] shortread base quality

[Martin Morgan]

On 08/27/2012 12:43 AM, David martin wrote:
> 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 ?

if the reads are all the same width (implied by the matrix above) then
as(quality(rfq), "matrix"); sorry about the misleading info. Martin

>
> 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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>>
>>
>
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