I am trying to run bedtools on my tab-delimited file but it still show me an error : It looks as though you have less than 3 columns at line: 1. Are you sure your files are tab-delimited?.
the command i run :
bedtools getfasta -fi fasta.fa -bed list.bed -fo results
my BED file looks like -->
scaffold_1000 9060 9912 scaffold_101084 600 2116 scaffold_101084 750 2330 scaffold_101084 800 2200 scaffold_101084 800 2300
what should I do next?
Check your bed file with
sed -n 'l'there you'll see all control characters.
Was the original file made in Windows? If so try