trouble in converting txt to bed file for bedtools

Question

[saadleeshehreen]

I tried to convert a .txt file to .bed file.

CONTIG  DNA_START   DNA_END     
NZ_AWYZ01001116.1   641 1875        
AWZB01001762.1  1975    2386        
NZ_AWZG01001811.1   646 18356       
AWYT01002050.1  2311    17133       
NZ_AWYV01001866.1   13969   14380       
NZ_AWYN01001907.1   17959   18370       
AWYR01002060.1  16722   17133       
AWYX01002140.1  8145    8556        
NZ_KK213231.1   7885    19297

I tried the following command

awk -F"[:-]" 'BEGIN{ OFS="\t"; }{ print $1, $2, $3; }' xx.txt > xx.bed

But bedtoos give the folowing error

Unexpected file format.  Please use tab-delimited BED, GFF, or VCF. Perhaps you have non-integer starts or ends at line 1?

I checked the file with the following command

  cat -A AcrIF3.bed | head
  CONTIG^IDNA_START^IDNA_END^I^I$

May be unnecessary characters are there.How to remove that? I also need to extract 5000 bp upstream and downstream sequences from the start and end coordinate. So also try the following code but same error as before.

awk '$2>$3 {print $1 "\t" $2 "\t" $3 "\t" $3-5001 "\t" $2+5000 "\tpep\t0\t-"}' xx.txt > xx.bed

Do you have any idea how can I convert it to a proper bed file? Cheers

Answer 1

[finswimmer]

Hello,

assuming your DNA_START and DNA_END coordinates are 0-based your txt file is already a valid bed file, if you remove or comment out (by adding a # at the line beginning) the first line.

fin swimmer

[saadleeshehreen]

Thanks. Your suggestion works

[ATpoint]

If it solved your peoblem, please mark the answer as accepted.