[Bioperl-l] Creating a fastq format file?

[Chris Fields]

On Apr 22, 2009, at 9:03 AM, 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

I think that's how it is defined, but I remember a while ago finding a  
formal definition of the format was a bit difficult.  Looks like that  
has been rectified:

http://maq.sourceforge.net/fastq.shtml

If the parser doesn't read Illumina FASTQ format feel free to post a  
bug report with some example data.  I'm sure this will be needed  
functionality in the future (and it shouldn't be too hard to add in).

chris