[BioC] about the quality score

[Martin Morgan]

On 01/11/2012 09:11 AM, wang peter wrote:
> i have data, like this
> @HWI-ST397_0000:5:1101:1110:2156#NTNTCG/1
> CAAGGAGCAGAGTGAGGTCTCTCCGCAGAGCGCCAAGGCAAAGCAGATGGTGGAGCTGCTCTACGAGACGGCGCACATTGCGTCTGGATTCCCGCCTG
> +HWI-ST397_0000:5:1101:1110:2156#NTNTCG/1
> gdgggegc_gffdeeggdgfggggdgbfadaeeeeefaefgcebebdffebbbbcg`gdgfgeeebgbddcbccbfdffcdcadbW_]]`]dd_bb\^
> reads<- readFastq(fastqfile);
> seqs<- sread(reads)
> it seems phred+64 system
>
> can i use the function:
> qual<- PhredQuality(quality(quality(reads)))
> i think can only read phred+32 system
>

 From ?readFastq, documenting the ... argument


      ...: Additional arguments. In particular, 'qualityType' and
           'filter':

           qualityType: Representation to be used for quality scores,
               must be one of 'Auto' (choose Phred-like if any character
               is ASCII-encoded as less than 59) 'FastqQuality'
               (Phred-like encoding), 'SFastqQuality' (Illumina
               encoding).

see also ?SolexaQuality

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