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Old 04-07-2011, 09:09 PM   #1
crh
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Default illumina to fastq

I'm new to working with NGS and we have some illumina reads we'd like to convert to fastq.
I've read the posts and tried to run the script qseq2fastq.pl on the samples w/o success.

the files have the following format which doesn't look quite like qseq:

USI-EAS39:1:1:2:1362#0/1:CTGGNTTCCACAGGCACATAGCCAAACCGGTGCCT:32 32 29 24 4 28 33 32 32 34 32 34 32 30 33 33 32 33 33 33 33 32 33 29 30 33 33 33 28 21 26 30 30 33 30

Appreciate any conversions ideas.

Charles
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Old 04-08-2011, 12:47 AM   #2
simonandrews
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The script below should convert this format of data into a fastq file with Illlumina 1.5 quality encoding (you can change the offset value on line 20 if you'd prefer Sanger format).

Code:
#!/usr/bin/perl
use warnings;
use strict;

my ($infile,$outfile) = @ARGV;

die "Must specify input and output filename\n" unless ($outfile);

open (IN,$infile) or die $!;
open (OUT,'>',$outfile) or die $!;

while (<IN>) {
  chomp;
  my @sections = split(/:/);

  my @qualities = split(/\s+/,$sections[-1]);

  my $quality_string = '';

  $quality_string .= chr($_ + 64) foreach (@qualities);

  my $seq_id = join(":",@sections[0..4]);
  print OUT '@',$seq_id,"\n",$sections[5],"\n+",$seq_id,"\n",$quality_string,"\n";

}

close OUT or die $!;
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Old 04-08-2011, 08:05 AM   #3
crh
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Thanks Simon,

what should the offset be for sanger fastq?

Charles
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Old 04-08-2011, 08:13 AM   #4
simonandrews
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Quote:
Originally Posted by crh View Post
what should the offset be for sanger fastq?
33 (apparently I need to add some more text otherwise the forum won't allow the post...)
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Old 04-08-2011, 09:26 AM   #5
crh
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Thanks again Simon - works fine.

Is the original format I have 'Gerald'?

Charles
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Old 04-08-2011, 10:21 AM   #6
ETHANol
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Biopython Seq I/O does these conversions. Pretty easy to use and with pretty good documentation.
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Old 04-08-2011, 01:11 PM   #7
kmcarr
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Quote:
Originally Posted by crh View Post
Thanks again Simon - works fine.

Is the original format I have 'Gerald'?

Charles
It's a very old Solexa format called SCARF (Solexa Compact ASCII Read Format). It's not used anymore. Is this data really old?

Last edited by kmcarr; 04-08-2011 at 01:14 PM. Reason: Expand acronym
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Old 04-14-2011, 02:02 PM   #8
crh
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I've used bioperl mostly, I'll check if they have seq conversions for illumina formats.
regarding the reads, I believe they are ~2 yrs old now.

thanks
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