How to convert eland file to BED format

huo · 01-19-2011, 11:35 AM

I have file in the following format. I want to use MACS but it requires bed format how can I convert my file to bed format

HWUSI-EAS230-R 1 2 4 713 1086 0 1 ACAAGTTACATAACCTCCCTGATATTATGAACCCAA aaabaaab`baaa``aa_`aa`aaaaaaaaa\^_`a c3.fa 188833058 R 36 118

Thanks,

selen · 01-19-2011, 11:43 AM

The following awk script converts sorted file to BED format that has 4 fields. You can update the script as you need...

# sortedToBed.awk
# Input : SORTED FILE
# Output : <Chromosome> <start position> <stop position> <strand>
# Usage
# awk -f sortedToBed.awk SORTED_INPUT_FILE_NAME > BED_OUTPUT_FILE_NAME

{OFS=" ";

len=length($9);

split($11, ref_chr, ".");

if ($13=="F") strand = "+";
else if($13=="R") strand = "-";
else strand = "None";

if (strand!="None")
print ref_chr[1], $12, $12+len, strand ;
}

Good Luck!
Selen

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01-19-2011, 11:35 AM	#1
huo Junior Member Location: PA Join Date: Jan 2011 Posts: 3	How to convert eland file to BED format I have file in the following format. I want to use MACS but it requires bed format how can I convert my file to bed format HWUSI-EAS230-R 1 2 4 713 1086 0 1 ACAAGTTACATAACCTCCCTGATATTATGAACCCAA aaabaaab`baaa``aa_`aa`aaaaaaaaa\^_`a c3.fa 188833058 R 36 118 Thanks,

01-19-2011, 11:43 AM	#2
selen Junior Member Location: Ohio Join Date: Dec 2010 Posts: 9	The following awk script converts sorted file to BED format that has 4 fields. You can update the script as you need... # sortedToBed.awk # Input : SORTED FILE # Output : <Chromosome> <start position> <stop position> <strand> # Usage # awk -f sortedToBed.awk SORTED_INPUT_FILE_NAME > BED_OUTPUT_FILE_NAME {OFS=" "; len=length($9); split($11, ref_chr, "."); if ($13=="F") strand = "+"; else if($13=="R") strand = "-"; else strand = "None"; if (strand!="None") print ref_chr[1], $12, $12+len, strand ; } Good Luck! Selen