[bio-tips] genomeCoverageBed: BAM2Wig

Last post  introduced the basic usage of genomeCoverageBed. Here is some update to deal with BAM2WIG processing. 

As the default output of genomeCoverageBed is formatted as following: 

chr start depth

However, WIG file format is different. The chromosome information is recorded in the header line:

variableStep chrom=chr1 span=1

Thus needed information exact work should be done. 

Here I share with you my homemade Perl script that manages to help you out. 

#!/usr/bin/perl -w
my ($in, $out) = @ARGV;
die $! && <DATA> unless (@ARGV ==2);

open IN, $in;
open OUT, ">$out";

print OUT "track type=wiggle_0 name="NAME" color=250,100,100 visibility=full autoScale=off viewLimits=0.0:99.0 yLineOnOff=off priority=10\n";
my $tmp = "NA";
while ( <IN> ) {
    chomp;
    my ($chr, $start, $v) = (split /\t/, $_)[0,1,2];
    my $tag = 0; 
    $tag = 1 if ($tmp eq $chr);
         if ($tag == 1 ){
             print OUT "$start\t$v\n";
         }
         elsif ($tag == 0){
              $tmp = $chr;
              print OUT "variableStep chrom=$chr span=1\n";
              print OUT "$start\t$v\n";
         }
}    

== End && reference

1. https://genome.ucsc.edu/goldenPath/help/wiggle.html
2. http://joseph.yy.blog.163.com/blog/static/509739592012824113338570/

 

== afters

thx god and thx girlfriend