Re: [maq-help] fastq input

[Joseph F. <jos...@gm...>]

> Does maq use the quality information in the fastq file for the map
> function?
>
yes!


>
> Is there to process fasta reads rather than fastq reads?

others on this list have suggested assigning uniform, fake qualities to
reads without qualities ... e.g.:

#!/usr/bin/perl
use strict;
my $usage = "\nusage: fakefastq.pl <input file (fasta format)> <output
file>\n\n
my $infile = shift or die $usage;
my $outfile = shift or die $usage;
open IN, "<$infile" or die $usage;
open OUT, ">$outfile" or die $usage;
my $header; my $sequence;
while (<IN>) {
        $header = $_;
        $sequence = <IN> or die $usage;
        $header =~ tr/>/@/;
        print OUT $header;
        print OUT $sequence;
        $header =~ tr/@/+/;
        print OUT $header;
        $sequence =~ tr/[A-Za-z]/:/; # ':' corresponds to a Sanger/phred
score of 25
        print OUT $sequence;
} # while
close IN; close OUT;




-- 
Joseph Fass
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