Codes and programs used in An et al. Nature Communications 2023.

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Distributed under the CC BY-NC-ND 4.0 license for personal and academic usage only.

Please refer to each directory (where wk.sh is the main script) for detailed information.

Notes:

1. Codes to process the raw fastq files (e.g., preprocessing, alignment, and duplicate-removal) are NOT covered here; you may need to install Ktrim, bowtie2, Msuite2, and samtools to perform these procedures;
2. bedtools and R are required to run these codes;
3. Nucleosome track is obtained from NucMap, here is the link to the file used in this work.