any one knows how to convert fastq illumina quality encoding 1.3-1.7 to 1.8+?

[Liangliang Gao]

It seems that fastqGroomer of Galaxy can do that.
It seems also that bioperl is able to do that.  I prefer cmd line options, cause I think Galaxy is not efficient at all.

Here is what I tried using Bioperl 1.6.9.

Let me know if you can help:

use strict;
use Bio::SeqIO;
use Data::Dumper;

my $file="test.fq"; # get the file name
my $outfile="test.convert.fq";
my $seqio_in=Bio::SeqIO->new(-file => "<$file", -format=>'fastq');
#print $seq_object ."\n";
my $seqio_out=Bio::SeqIO->new(-file=>"> $outfile",-format=>'fastq',-qualtype=>'sanger');

while (my $seq=$seqio_in->next_seq){
        $seqio_out->write_seq($seq);
        print Dumper ($seqio_out);
}


############## I checked the output file, the formats were not changed. Any clue? Sorry that this is not related too much with SPADA, but it is pretty important for me.

[Peng Zhou]

Hi Liang,

Unfortunately I don't have this experience, but here is the forum you should really check and post your question on:

http://seqanswers.com/forums/forumdisplay.php?f=18

Peng,

[Liangliang Gao]

I figured it out (see below). Thanks for your suggestions!

my $seqio_in=Bio::SeqIO->new(-file => "<$file", -format=>'fastq', -variant=>'illumina');
my $seqio_out=Bio::SeqIO->new(-file=>"> $outfile",-format=>'fastq',-variant=>'sanger');