[Bioperl-l] Conversion of Phred 33 -> Phred 64 quality

[Roy Chaudhuri]

Hi Mark,

Here's the relevant bit of the manual:
http://search.cpan.org/~cjfields/BioPerl/Bio/SeqIO/fastq.pm#FASTQ_and_Bio::Seq::Quality_mapping

There's also this article, which goes into the issue in depth:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2847217

A short Illumina->Sanger fastq converter would be:

use Bio::SeqIO;
my $in=Bio::SeqIO->new(-file=>$ARGV[0], -format=>'fastq', 
-variant=>'illumina');
my $out=Bio::SeqIO->new(-format=>'fastq', -variant=>'sanger');
$out->write_seq($_) while $_=$in->next_seq;

Cheers,
Roy.

On 26/01/2015 14:23, Mark A. Jensen wrote:
> Hi folks,
> I know I could RTFM, but maybe someone knows off the top of their head:
> I understand that Illumina at one time made a switch in the constant
> added to quality scores to generate the FASTQ that comes off their
> instruments. This leads to a certain incomparability of data before and
> after that switch. This is about all I know of the issue; does anyone
> here have experience with this? Are there any BP modules that do this
> translation?
> much appreciated-
> MAJ
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