Unusual use of .ab1 files from an ABI capillary sequencer -- help

[john1923]

Hi,

I want to extract the "trace data" from the ab1 file, without calling bases. the traces from my experiment will look like this. With peaks scattered randomly throughout the trace. (It is not a normal sequencing read)

__________________|_______|______________________________
_______|____________________________________________|____


So I want the raw output from each channel, as an array.

Then I want to analyse it with Perl.

Has anyone got any ideas.

If you are interested, The experiment is RSCA, Reference Strand Conformational Analysis.

Thank you in advance.

[kmcarr]

Have you checked out the Perl module Bio::Trace::ABIF? The trace() or raw_trace() methods sound like what you're looking for.

[john1923]

Thanks, that looks like it will do what I want.

[john1923]

Thank you

ABIF Worked perfectly, here is the magic code.

use Bio::Trace::ABIF;

my $abif = Bio::Trace::ABIF->new();
$abif->open_abif('A02_736a.fsa');

print $abif->sample_name(), "\n";
print $abif->raw_data_for_channel(1);

$abif->close_abif();

Now I have to do the analysis, but this should be fairly straight-forwards.