# Description

CENP-A CUT&RUN (5 kbp)

# Methods

CENP-A and IgG CUT&RUN data (250-bp, paired-end) were generated for each cell line, trimmed using Sickle (v1.33) to remove low-quality bases, trimmed with cutadapt (v5.0) to remove adapters, and aligned to the relevant assembly using BWA (v0.7.17) with the following parameters: bwa mem -t {num_of_threads} -k 50 -c 1000000 {index} read1.fq read2.fq | samtools view -bS -F 2308 | samtools sort -m 8G -T tmp -o {output.bam}. The CENP-A signal was normalized with the IgG signal using deepTools (v3.5.5) and the following command: bamCompare -b1 {CENP-A.bam} -b2 {IgG.bam} --operation ratio --binSize 5000 --minMappingQuality 1 -p 20 -o {output.bw}.

# Credits

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