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.
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>