<p dir="ltr">Roy, you are awesome, as usual-<br>
Much appreciated! MAJ</p>
<br/><div class="cm_quote" style=" color: #787878">On Mon, Jan 26, 2015 at 9:51 AM, Roy Chaudhuri <<a href="mailto:roy.chaudhuri@gmail.com">roy.chaudhuri@gmail.com</a>> wrote:</div><br><div id="oldcontent" style="background-color: rgb(255, 255, 255); background-position: initial initial; background-repeat: initial initial;"><blockquote style=""><p dir="ltr">Hi Mark,
<br>
<br>
Here's the relevant bit of the manual:
<br>
http://search.cpan.org/~cjfields/BioPerl/Bio/SeqIO/fastq.pm#FASTQ_and_Bio::Seq::Quality_mapping
<br>
<br>
There's also this article, which goes into the issue in depth:
<br>
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2847217
<br>
<br>
A short Illumina->Sanger fastq converter would be:
<br>
<br>
use Bio::SeqIO;
<br>
my $in=Bio::SeqIO->new(-file=>$ARGV[0], -format=>'fastq',
<br>
-variant=>'illumina');
<br>
my $out=Bio::SeqIO->new(-format=>'fastq', -variant=>'sanger');
<br>
$out->write_seq($_) while $_=$in->next_seq;
<br>
<br>
Cheers,
<br>
Roy.
<br>
<br>
On 26/01/2015 14:23, Mark A. Jensen wrote:
<br>
> Hi folks,
<br>
> I know I could RTFM, but maybe someone knows off the top of their head:
<br>
> I understand that Illumina at one time made a switch in the constant
<br>
> added to quality scores to generate the FASTQ that comes off their
<br>
> instruments. This leads to a certain incomparability of data before and
<br>
> after that switch. This is about all I know of the issue; does anyone
<br>
> here have experience with this? Are there any BP modules that do this
<br>
> translation?
<br>
> much appreciated-
<br>
> MAJ
<br>
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<br>
</p>
</blockquote></div>