Hi, I have manually created a bed file to extract the sequences from a fasta file. But it is showing the following error message. How can I solve it?
-bash-4.2$ cat pAcr_extract.bed PSE305_1 20001 20479 PSE305_1 20306 20479 PSE305_1 20001 20303 AZPAE14907_contig_18_1 20001 20479 AZPAE14907_contig_18_1 20001 20303 WH-SGI-V-07178_contig3_1 20001 20303 WH-SGI-V-07178_contig3_1 20306 20479 bash-4.2$ bedtools getfasta -fi pAcr_extract.fasta -bed pAcr_extract.bed -fo pAcr_extract.fasta.out It looks as though you have less than 3 columns at line: 1. Are you sure your files are tab-delimited?