Nucleosomics-focused scripts for analysis of cfDNA, nucleosome positioining in vivo and related aspects. This repository hosts few scripts associated with our current manuscripts on nucleosome repositioning in cancer.
License
This software belongs to the Laboratory of Gene Regulation at the University of Essex (generegulation.org) and is availabe to external users under CC-BY-NC-ND licence (non-commercial use only, no derivateves, full attribution required, including the name of the package, cfDNAtools). Please provide references to this repository and to the following publications:
Piroeva K. V., McDonald C., Xanthopoulos C., Fox C., Clarkson C. T., Mallm J.-P., Vainshtein Y., Ruje L., Klett L. C., Stilgenbauer S., Mertens D., Kostareli E., Rippe K. and Teif V. B. (2023) Nucleosome repositioning in chronic lymphocytic leukaemia. Genome Research 33, 1649-1661.
Shtumpf M., Jeong S., Bikova M., Mamayusupova H., Ruje L. and Teif V.B. (2024) Aging clock based on nucleosome reorganisation derived from cell-free DNA. Aging Cell 23, e14100
fragment_length_histogram.r - takes as input a NucTools-compatible BED file with paired-end reads which contains a column with DNA fragment sizes, and outputs the distribution of fragment lengths in the form of a histogram. Example command:
Rscript fragment_length_histogram.r <input_bed_file.bed> <output_file.txt>
extract_nuc_sizes.pl - takes as input a NucTools-compatible BED file with paired-end reads which contains a column with DNA fragment sizes, and extracts to a new BED file only the fragments within a set range of sizes. Example command:
perl extract_nuc_sizes.pl -input=<in.bed> -output=<out.bed> -min=<min_fragment_size> -max=<max_fragment_size>
methylationThresholds.pl - takes as input a Bismark-compatible BED file with DNA methylation beta-values as a separate column, and extracts to a new BED file only the nucleotides which have methylation levels between two thresholds. Example command:
perl methylationThresholds.pl -input=<in.bed> -output=<out.bed> -threshold1=<minimum_methylation> -threshold2=<maximum_methylation>
bed2occupancy.v3d.methyl.pl - takes as input a Bismark-compatible BED file with DNA methylation beta-values as a separate column, and outputs a NucTools-compatible "occupancy" file with normalised DNA methylation score per each nucleotide. Example command:
perl bed2occupancy.v3d.methyl.pl <chr1.bed> <chr1.occ>