public
Description: Processing Abnormal Read-Pairs
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Clone URL: git://github.com/jandot/parp.git
Jan Aerts (author)
Fri Jul 24 06:34:11 -0700 2009
parp /
name age message
file .gitignore Wed Jun 03 02:41:14 -0700 2009 Added .gitignore [Jan Aerts]
file README.textile Fri Dec 05 14:20:29 -0800 2008 Changed title of README [Jan Aerts]
directory data/ Thu Jul 09 05:44:31 -0700 2009 Removed unused lines from config file [Jan Aerts]
directory lib/ Fri Jul 24 06:34:11 -0700 2009 Fixed bug [Jan Aerts]
directory pARP.app/ Thu Jul 09 05:40:50 -0700 2009 Recreated new pARP applications [Jan Aerts]
file parp.rb Wed Jul 08 03:41:40 -0700 2009 Moved config.yml to data-directory. Necessary f... [Jan Aerts]
directory scripts/ Fri Mar 06 07:52:11 -0800 2009 Expanded filter a bit [Jan Aerts]
directory test/ Fri Jul 03 05:46:02 -0700 2009 Added test for calculating bp_position_under_mo... [Jan Aerts]
directory vendor/ Tue Jul 07 06:01:14 -0700 2009 Added vendor directory [Jan Aerts]
README.textile

pARP — Abnormal ReadPair Visualization

A tool for visualizing abnormal read pairs (i.e. too far apart, forward-forward or reverse-reverse).

One of the ways to identify structural variation in a genome is to look at mapping of a read-pair library on a reference genome. Any read-pair (i.e. the ends of the same clone) normally maps in a forward-reverse orientation at a distance from each other that corresponds to the insert size of the clone library. Structural variation between the reference genome used for mapping and the genome used to create the clone library will cause the reads to map in the wrong orientation (i.e. forward-forward or reverse-reverse; indicating an inversion) or at too large or too small a distance (indicating an insertion or deletion in the sample, respectively).

pARP basically displays raw read pair mapping data and does not make any assumptions on models as might be required when doing a statistical analysis of the same data. By showing a birds’ eye view it helps in interpreting what structural variations are present.