# Description

ONT 5mC

# Methods

ONT data was basecalled with Guppy (v6.5.7), and the resulting methylbam was converted to a bedMethyl file using the following command: modbam2bed -e -m 5mC --cpg -t {num_of_threads} {assembly.fa} {input.bam} > {output.bed}. This was converted to a bedGraph with the following command: awk 'BEGIN {OFS="\t"}; {print $1, $2, $3, $11}' {input.bed} | grep -v "nan" | sort -k1,1 -k2,2n > {output.bedgraph}. The bedGraph was then converted to a bigWig with the following command: bedGraphToBigWig {input.bedgraph} {assembly.fa.fai} {output.bw}.

# Credits

Gabrielle Hartley <gabrielle.hartley@uconn.edu>, Glennis A. Logsdon <glogsdon@pennmedicine.upenn.edu>, Rachel O'Neill <rachel.oneill@uconn.edu>