This script calls the program bigWigSummary to extract enrichment from a bunch of bigWig files (they can be a lot of Chip-Seq experiments for example) for a set of intervals stored in a bed file. You need to files to run the script, a bed file containing

bulk-bigwig.pl

# author : Radhouane Aniba 

#!/usr/bin/perl -w
 
@files = <FOLDER_FOR_BigWigs/*.bigWig>;

# For this example we have 4 bigwig files 

open(BEDFILE, "FILENAME");
while(<BEDFILE>)
 {
 # Good practice to store $_ value because
 # subsequent operations may change it.
 my($line) = $_;

 # Good practice to always strip the trailing
 # newline from the line.
 chomp($line);

 # Convert the line to upper case.
 #$line =~ tr/[a-z]/[A-Z]/;

 # Print the line to the screen and add a newline
 
 my @coord = split(/\t/, $line);
 my $a = $coord[1];
 my $b = $coord[2];
 print "$coord[0] \t $a \t $b \t $coord[3] \t $coord[4] \t";
 
my $i = 0;
# in the while loop you have to always put as limit (#of files -1)
 while($i <= 3) {
   $tmp1 = getIntervalScore($files[$i],$coord[0],$a,$b,1);
   chomp($tmp1);
   if($i == 3){ 
   print "$tmp1 \n";
   }else{print "$tmp1 \t";}
 $i++;
 } 

 } 

close (BEDFILE);



sub getIntervalScore {
    ($bwfile, $chr, $start, $end, $step) = @_;

    @score = `./bigWigSummary $bwfile $chr $start $end $step 2>&1`;
#print "RawData/bigWigSummary $bwfile $chr $start $end $step 2>&1";
    $scoreval = $score[0];
    if ($scoreval =~ m/no/){$scoreval = 0;}
    return $scoreval;
}