[Bioperl-l] Creating a fastq format file?
cjfields at illinois.edu
Wed Apr 22 10:50:47 EDT 2009
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:
>> 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?
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:
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).
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