[Bioperl-l] Error converting FASTQ(ASCII-64 ) to Sanger(ASCII-33) using Bio:SeqIO
Abhishek Pratap
abhishek.vit at gmail.com
Fri Jul 9 15:02:09 UTC 2010
Hi (Chris)
I feel I might be hitting a bug or missing something. I am trying to convert
a raw FASTQ from ASCII-64 to ASCII-33. I am copying the actual code and IO
for more clarity. I think the quality line is missing and the read is
breaking into two lines.
Any obvious mistakes ?
Thanks!
-Abhi
## Reading the FASTQ ASCII-64 file
my $in = Bio::SeqIO->new( -format => 'fastq',
-variant => 'illumina',
-file => "<$in_fastq_file",
);
## File Handle for writing ASCII-33 (sanger) standard format
my $out = Bio::SeqIO->new ( -format => 'fastq',
-variant => 'sanger',
-file => ">$out_fastq_file",
);
while (my $oneread = $in->next_seq){
$out->write_seq($oneread);
}
Output:
>HWI-EAS397_0006:6:1:1023:19461#0/1
ATGTGCTGCTGGCTTCGGTTTGCCAGTATTTTATTGAGGATTTTTGCATCAATGTCATCA
AGGATATTGGTCTAA
Input:
@HWI-EAS397_0006:6:1:1023:19461#0/1
ATGTGCTGCTGGCTTCGGTTTGCCAGTATTTTATTGAGGATTTTTGCATCAATGTCATCAAGGATATTGGTCTAA
+HWI-EAS397_0006:6:1:1023:19461#0/1
^aYa^\a^aaaa\]a^^^^^]]]^L^Y]]]aa\`YZ^a]]a[a^^^^^`I^^^`]aaaa]]^]R`W^``^BBBBB
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