thank you very much
i think this method is not reliable
if the data is high quality, no nt is low , like 59.
they will be thought as SFastqQuality.

i would u like to see if some score is higher than 80, then choose
SFastqQuality.


On Thu, May 15, 2014 at 3:56 AM, Martin Morgan <mtmorgan@fhcrc.org> wrote:

> On 05/14/2014 11:17 AM, Wang Peter wrote:
>
>> the coding can works well on many data.
>> but when it works on 12 lines, i met such a problem
>>
>> how can the function tell the score if 33 or 64 system?
>>
>> library(ShortRead);
>> reads <- readFastq(fastqfile);
>> seqs <- sread(reads);
>> score_sys = data.class(quality(reads));
>> cat("the quality score system
>> (SFastqQuality=Phred+64,FastqQuality=Phred+33) is",score_sys,"\n")
>>
>>
>> the output is:
>> the quality score system (SFastqQuality=Phred+64,FastqQuality=Phred+33)
>> is
>> SFastqQuality
>> but it is really the FastqQuality=Phred+33
>>
>> @HISEQ04:126:C343UACXX:8:1103:15851:74641 1:N:0:ACAGTG
>> GGCCTCTCAATGTCAAGGGATCGACGGCAGATATCATAGATGGCCTCATTGTCCAAGAGA
>> ACTGCGACATCTGTGTGCTCGAGCAAGGAATGAGTGGAAAG
>> +
>> BBBFFFFFFFFFFFFIIIIIIIIIIIIIIIFIIIIIIIIIIIIIIIIIIIIIIIIIIFFF
>> FFFFFFBFFFFBFFFFFFFFFFFFFFFFFFFFFFBFFFBFB
>> @HISEQ04:126:C343UACXX:8:1103:16187:74529 1:N:0:ACAGTG
>> CAATTCTAGCTACTGGAGCTGTCCATTTGCCGCGCAGGCACTGAAGATAGAACATCGATC
>> GAGTCAACCTCTACCTGCATTAGGTGACTGCTGAGAGCTCC
>> +
>> BBBFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFFFF
>> FFFBFFFFFFFFFFFFFBFFFFFFBFFFFFFFFFFFFFFFF
>> @HISEQ04:126:C343UACXX:8:1103:16244:74553 1:N:0:ACAGTG
>> GCCGAAGCATTTTTGGCTTCTGTAAGGTTGTACATATGAAGCAGATTGCTCCAGCTTGGA
>> AGAGTCATGTTTGTGACGAGAGAACTGGCTACAGCTCCAGG
>> +
>> BBBFFFFFFFFFFIIIIIIIIIIIIIIFFIFIIIIIIFIIIIIIIIIIIIIIIIIIIIII
>> IIIIFFFIIFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFF
>>
>>
>>
> From the help page
>
>   ?readFastq
>
> the 'qualityType' argument is described as
>
>           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).
>
> 'Auto' is the default, none of the ASCII-encoded quality characters is
> less than 59, hence choose SFastqQuality.
>
> Invoke the command with the information about encoding if known,
>
>   readFastq(fastqfile, qualityType="FastqQuality")
>
> See this previous post
>
>   https://stat.ethz.ch/pipermail/bioconductor/2012-September/048172.html
>
> --
> Computational Biology / Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N.
> PO Box 19024 Seattle, WA 98109
>
> Location: Arnold Building M1 B861
> Phone: (206) 667-2793
>



-- 
shan gao
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Boyce Thompson Institute for Plant Research
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