Making a motif BED file.

Downstream analysis may require a BED file to select motifs of interest. For example, selecting GATC motifs in E. coli. This command requires a reference sequence in FASTA a motif to find, which can include IUPAC ambiguous bases and a position within the motif.

The following command would make a BED file for CG motifs.

modkit motif-bed reference.fasta CG 0 1> cg_modifs.bed

The output is directed to standard out.