CE statistic computation code

DOWNLOAD

The code is available here.

USAGE

programs to run:

getMateStats.all_lib.perl <reads.placed file> <matepair by readname file>  <library info file>

<reads.placed file> -- reads.placed file in Washington University format
<matepair by readname file> -- mates file in the form:
    read1 read2 reported_separation
<library info file> -- file with computed library information, one library per line, space separated:
    reported_separation computed_separation computed_stdev

The getMateStats.all_lib.perl  produces a file ce_statistic.txt with a value of ce statistic for every mated read

my_compute_statistic_output_gaps.pl ce_statistic.txt <threshold> -- finds CE problem points for a given threshold (3 is suggested) and outputs them to STDOUT.

supplementary programs:

compute_statistic_all.perl
getMateStats.wReadInfoLine.pt2.perl
getMateStats.wReadInfoLine.pt4.perl
sort_ce_file.pl
getMateStats.pt3.perl
getMateStats.wReadInfoLine.pt5.perl
getMateStats.wReadInfoLine.pt1.perl
getMateStats.wReadInfoLine.pt6.perl