[Bioperl-l] Creating a fastq format file?
j_martin at lbl.gov
Wed Apr 22 11:58:15 EDT 2009
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:
>> 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
>> Any suggestions? What am I missing?
> 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?
No they aren't the same, Illumina still encodes the ascii as value + 64
and Sanger as value + 33.
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