SEQanswers

Go Back   SEQanswers > General

Similar Threads
Thread Thread Starter Forum Replies Last Post
Doubt about .abi files and .fasta files fc35802 Bioinformatics 2 02-28-2012 11:05 AM
Unusual QV on F3 vv85 SOLiD 0 07-27-2011 10:10 AM
Capillary sequencer market. pmiguel Sanger/Dye Terminator 4 07-02-2011 08:49 PM
batch editing of ABI files raymoniz General 6 09-29-2010 01:28 PM
In Sequence: ABI, Illumina, Former Lawyer Fail to Settle IP-Ownership Suit; ABI Seeks Newsbot! Illumina/Solexa 0 04-01-2008 02:14 PM

Reply
 
Thread Tools
Old 03-23-2012, 06:27 AM   #1
john1923
Junior Member
 
Location: Cambridge

Join Date: Apr 2011
Posts: 7
Default Unusual use of .ab1 files from an ABI capillary sequencer -- help

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.
john1923 is offline   Reply With Quote
Old 03-23-2012, 06:57 AM   #2
kmcarr
Senior Member
 
Location: USA, Midwest

Join Date: May 2008
Posts: 1,178
Default

Have you checked out the Perl module Bio::Trace::ABIF? The trace() or raw_trace() methods sound like what you're looking for.
kmcarr is offline   Reply With Quote
Old 03-23-2012, 07:09 AM   #3
john1923
Junior Member
 
Location: Cambridge

Join Date: Apr 2011
Posts: 7
Default

Thanks, that looks like it will do what I want.
john1923 is offline   Reply With Quote
Old 03-23-2012, 09:39 AM   #4
john1923
Junior Member
 
Location: Cambridge

Join Date: Apr 2011
Posts: 7
Default

Thank you

ABIF Worked perfectly, here is the magic code.

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.
john1923 is offline   Reply With Quote
Reply

Tags
ab1, abi, perl, sanger, sanger format

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 01:50 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO