Codes and programs used in An et al. Nature Communications 2023.
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:
- 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;
- bedtools and R are required to run these codes;
- Nucleosome track is obtained from NucMap, here is the link to the file used in this work.