[Bioperl-l] Creating a fastq format file?

[Joel Martin]

On Wed, Apr 22, 2009 at 09:03:57AM -0500, Michael Muratet wrote:
>
> On Apr 22, 2009, at 8:32 AM, Dan Bolser wrote:
>
>> In the Bio::SeqIO::fastq page:
>>
>> http://search.cpan.org/~cjfields/BioPerl-1.6.0/Bio/SeqIO/fastq.pm#write_seq
>>
>>
>> I read:
>>
>> "This object can transform Bio::Seq and Bio::Seq::Quality objects to
>> and from fastq flat file databases."
>>
>> I'm not sure how to code the link between the fastq IO object and the
>> qual object that I have created using the code from the previous
>> thread...
>>
>> Any suggestions? What am I missing?
>
> Howdy
>
> This might be a good place to ask the question: having looked at the 
> fastq.pm page, is the fastq format defined (only) by a "@'" followed by a 
> sequence line and a "+" header followed by a quality line and the two 
> headers have to agree? Now that Illumina is using phred scaling, are 
> 'Sanger' and 'Illumina' versions the same?
>
> Thanks
>
> Mike

No they aren't the same, Illumina still encodes the ascii as value + 64
and Sanger as value + 33. 

Joel