This repository contains various programs that we developed for our paper Circulating DNA reveals nucleosome occupancy patterns that are associated with nucleosome-DNA affinity and are affected in cancer. The different codes are found in folders corresponding to the main steps of this study.
There is a folder referenceFile with parameter files and
a large text file masterScript_v3 that illustrates how these codes were
executed (in our setting). There is also a zipped file named
compiled-selection.zip, which contains all the candidate WPS peaks, i.e.,
~9 million peaks. The actual collection of WPNs used in most analyses is limited
to all the peaks in this file that display a width larger than or equal to 147
bp and smaller than 300 bp,
which results in ~5 million peaks.
In a few cases, some programs were used in several parts of our work. We put such programs in one folder only.
The Savitzky-Golay filter code (sgfilter.c and sgfilter.h) in the WPNAcomputation folder
is a slightly modified version of the excellent implementation proposed by Fredrik
Jonsson. Instructions to compile the code are in the sgfilter.pdf file.
The C++ codes were compiled with basic options, for instance
g++ -O2 -o normalize normalize-1.cpp