Bed file conversion doubts

[seq_GA]

I have used BEDtools to convert bam file into bed format.
How to convert bed to wig file? Thanks.

[adamdeluca]

use genomeCoverageBed (with the -bg option) from bed tools to convert bed->bedgraph
then use bedGraphToBigWig from UCSC to convert bedgraph->bigWig

[biznatch]

Perl script for .bed to .wig

Disclaimer: I started doing Chip-seq analysis about 3 weeks ago, and have a 2 week class and about 2 months experience using Perl. Nevertheless, here is my attempt at a Perl script that converts .bed files to .wig. It uses single end 51bp reads.

I'd appreciate any advice, particularly if anyone can point out if this isn't doing what I think it's doing

#!/usr/bin/perl -w
use strict;

#This script takes in a standard .bed file (chromstart in column 2, chromend in column 3) and converts it to a .wig file

my $file = $ARGV[0]; my $file2 = substr($file, 0, - 4); my $outfile = "$file2.wig";	#get input filename, replace extension
my $bp = 0;
my @data = 0;
my $read = 0;
my @hits = ();


open (IN, "<$file") || die "the file $file did not open $!\n";		#open file specified by user
open (OUT, ">> $outfile") || die " $!\n";				#open the output file
	
while(<IN>){					#for each line
	my @column = split("\t");  		#split on tab
	my $start = $column[1];			#start bp is column 2
	my $end = $column[2];			#end bp is column 3
	chomp($end);
	my $length = $end-$start;		#determinet length of read
	$read++;				#increase counter by 1

#	print "Read $read starts at $start and ends at $end and is $length bp long.\n";		#troubleshooting line to make sure each line is being read correctly

	for(my $bp = $start; $bp <= $end; $bp++){		#from first to last bp of read
		$hits[$bp]++;					#increment corresponding position by one
#		print "bp $bp now has @hits[$bp] hit(s)\n";	#troubleshooting line to monitor hits at each bp
	}
}

close IN;

my $count = 0;
my $item = 0;
my $site = 0;

foreach $item (@hits){				#for each line of hits
	$site++;				#increase the count at that site
	if (defined $item){			#will print out for all non-zero sites
		print OUT "$site\t$item\n";
		$count++;
	}
}

print "There were $read reads.\n$count sites (individual bp's) had at least one hit.\n";

close OUT;

[sameet]

Is there any way to convert from *.wig* to *.bed*?

[adamdeluca]

Is there any way to convert from *.wig* to *.bed*?

bigWigToBedGraph

http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/