[Bioperl-l] Creating a fastq format file?
mmuratet at hudsonalpha.org
Wed Apr 22 10:03:57 EDT 2009
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?
> 2009/4/22 Dan Bolser <dan.bolser at gmail.com>:
>> Creating a fastq format file from fasta and 'fasta quality file'?
>> I'm sure this is easy, but I'm still not able to 'think bioperl'...
>> I have a 'fasta quality file' and a fasta file, and I would like to
>> output a fastq file. I followed the discussion on the previous thread
>> With the conclusion seeming to be 'just do it'. Could someone point
>> at a way to do this, or was that suggestion an error? i.e. the poster
>> was working out a way to create a fastq the only way possible...
>> I get the feeling that this should be a one-liner, but perhaps the
>> above thread was demonstrating the code I need to copy.
>> Thanks for any suggestions,
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
More information about the Bioperl-l