# Description

CENP-A DiMeLo-seq

# Methods

CENP-A DiMelo-seq data and negative DiMeLo-seq data (generated without an antibody) were aligned to the relevant genome assembly using minimap2 (v2.26) and the following command: minimap2 -ax lr:hq -y -t {num_of_threads} -I 8g. The BAM file was converted to a bedMethyl file using modbam2bed and the following command: modbam2bed -e -m 6mA -t {num_of_threads} {assembly.fa} --mod_threshold=0.8 {input.bam} > {output.bed}. Then, the bedMethyl file 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 CENP-A and negative bedGraphs were combined using bedtools (v2.31.1) and the following command: unionBedGraphs -g {assembly.fa} -i {CENP-A.bedgraph} {negative.bedgraph} > {output.union.bedgraph}. The negative basecalls were then substracted from the CENP-A basecalls with the following command: awk 'BEGIN {OFS="\t"}; {print $1,$2,$3,$4-$5}' {input.union.bedgraph} | sort -k1,1 -k2,2n > {subtract.bedgraph}. The bedGraph was then converted to a bigWig.

# Credits

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