NAME

MyShortRead::MyShortRead - My Perl library to deal with nextgen short read data.

SYNOPSIS

            

              
              
use MyShortRead::MyShortRead;
my $compare_res = &compare2($interval_a, $interval_b, $compare_by);
my $boolean = &overlap2(\@interval1, \@interval2);
my $GC_percent = &strGCPercent($DNA_seq);
&bin_genome_count($bedfile, $bin_size, $chrom_len, $fragsize, \@bin_vector);
&bin_genome_count_direction($bedfile, $bin_size, $chrom_len, $fragsize, \@bin_vector);
my %chrom_tbl = &read_chrlen_tbl($chrom_filename);
my @chrom_list = &read_chrlen_ordered($chrom_filename);
my ($n_reads, $ref_hash_chrom_sepFileName) = &sep_chrom_bed($bedfile, @chrom_name);
&del_chrfile(@chrom_sepFiles);
my $compare_res = &order_chr($chrom_name_a, $chrom_name_b);
            
          

DESCRIPTION

            

              
              
This module contains a few functions that I created to perform some operations on 
short read data from next-generation sequencing machines. They include separate a
BED file according to chromosomes; bin genome and count the number of reads; compare
two genomic intervals and determine which one comes first(on the left side).
            
          

EXPORT

            

              
              
compare2
overlap2
strGCPercent
bin_genome_count
bin_genome_count_direction
read_chrlen_tbl
read_chrlen_ordered
sep_chrom_bed
del_chrfile
order_chr
            
          

SEE ALSO

MyShortRead::ChromBed MyShortRead::SRBed

AUTHOR

Li Shen, <shenli.sam@gmail.com>

COPYRIGHT AND LICENSE

Copyright (C) 2010-2013 by Li Shen

diffReps goes under GNU GPL v3: http://www.gnu.org/licenses/gpl.html