[BioC] how to get the quality score system information from the reads

[Martin Morgan]

On 11/8/2012 4:18 PM, wang peter wrote:
> i remember the shortread package can identify the read score system is
> phred+33 or 64
>
> if i use
>
> reads <- yield(inFh)
> or reads <- readFastq(fastqfile);\
>
> how can i get that information from the reads?

quality(reads) returns an object that displays either

class: SFastqQuality

in which case the reads are 'Solexa' (phred + 64) encoded or

class: FastqQuality

in which case they are phred + 33 encoded. ?readFastq contains information on this.

Martin

>
> thank you
>


-- 
Dr. Martin Morgan, PhD
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109