Bowtie output to BED format

[captainentropy]

Thanks dnewkirk

I always ignore the dates. A question with an answer many months after the OP is still likely to be valuable for someone out there.

[dnewkirk]

I had posted per the original question without noticing the dates . Either or works, but it may help someone who isn't as familiar with Perl on how to convert between file formats.

[captainentropy]

Thanks dnewkirk, could you tell us what would be the advantage to using your perl script would be over an awk command? I'm not criticizing, just wondering. I use an awk command in a shell script to convert.

[dnewkirk]

#!/usr/bin/perl

use strict;
use warnings;

# get file names from the command line
my ($input, $output) = @ARGV;

# exceptions and usage
if (!defined $input or !defined $output) {
    die "Usage: bedFromBowtie.pl <input> <output>\n";
}

# open the input/output file
open my $out, ">", "$output" or die "Cannot open $output: $!\n";
open my $in, "<", "$input" or die "Cannot open $input: $!\n";

while ( <$in> ) {
    chomp;
    my (undef, $strand, $chr, $start, $sequence) = split "\t"; # assumes standard bowtie output
    my @sequence = split '', $sequence; # extra work, but allows for variable-length sequences
    my $length = @sequence;
    my $end;
    if ($strand eq '+') {
        $end = $start + $length - 1;
    }
    elsif ($strand eq '-') {
        $end = $start;
        $start = $end - $length + 1;
    }
    else {
        die "We have a formatting problem: strand is set to $strand\n";
    }
    print $out "$chr\t$start\t$end\tU0\t0\t$strand\n";
}

print "Done!\n";

close $in; close $out; exit;

[captainentropy]

Hi,

what is H=111 $H,$2 doing in your command?

Thanks

With the H=111 and $H I think arun is just setting an awk variable. I'm not sure what use it has actually in this case. The exact same result can be achieved with "...$1,111,$2}..." The 5th column in a bed file is for a score to set the level of gray for each item (http://genome.ucsc.edu/FAQ/FAQformat.html#format1).

$2 is the 6th column - the strand the read maps to.

If you wanted a random score for column 5 you could use this in the awk command instead:
"...$1,int(rand()*1000),$2}..."

[ysccseqanswers]

awk 'BEGIN {FS= "\t"; OFS="\t"} {print $3, $4, $4+length($5)-1, $1,
H=111 $H, $2}' Bowtie_output > Bowtie_output.BED

This is a shell command, give this command in "$" prompt, it will convert your input file (Bowtie_output) file to BED format (Bowtie_output.BED)

Hi,

what is H=111 $H,$2 doing in your command?

Thanks

[arun]

awk 'BEGIN {FS= "\t"; OFS="\t"} {print $3, $4, $4+length($5)-1, $1,
H=111 $H, $2}' Bowtie_output > Bowtie_output.BED

This is a shell command, give this command in "$" prompt, it will convert your input file (Bowtie_output) file to BED format (Bowtie_output.BED)

[arun]

bowtie to BED format

awk 'BEGIN {FS= "\t"; OFS="\t"} {print $3, $4, $4+length($5)-1, $1,
H=111 $H, $2}' Bowtie_output > Bowtie_output.BED

This is a shell command, give this command in "$" prompt, it will convert your input file (Bowtie_output) file to BED format (Bowtie_output.BED)

[mattanswers]

Hi polsum,

Do you know any Perl ? I have a perl script that will convert bowtie .map file to a .bed file, but you may have to know a little perl to work with it.

[steven]

Ok I just found out. Save the bowtie output in Sam format, convert it to Bam format by samtools and convert Bam to BED by Bedtools.

hi, thanks for the question + answer and good parsing..

[polsum]

Hi - Can any one please suggest a method to convert Bowtie output to BED format? Is there a bioperl script or any software for that?

thanks in advance.

Ok I just found out. Save the bowtie output in Sam format, convert it to Bam format by samtools and convert Bam to BED by Bedtools.

[polsum]

Hi - Can any one please suggest a method to convert Bowtie output to BED format? Is there a bioperl script or any software for that?

thanks in advance.