Originally posted by Oxygen81
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Just looking at James Bonfield's code in post 7 (without testing it), I'd say try changing the part that goes:
} else {
my @qa = split('\t', $q);
@qual = map {[split()]->[$hmap{substr($seq, $i++, 1)}]} @qa;
}
to
} else {
my @qual = split('\s', $q);
}
That might work.
Edit: Note that the script below works if you have a single .qual file, and a single .seq file. Bonfield's script takes all the files in the folder, so if you point it at the run directory, it does all 300 tiles for all 8 lanes.
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