Nucleosome ctDNA analysis code

Usage: extract this to a (linux) server. Build the cproj files in tools/cproj using cmake.

Contents

• pipeline/arr-paired-reads: Create fragments from paired DNA reads
• pipeline/make-nuc-file: Create a nucleosome reference file from a nucleosome BED file.
• pipeline/assign-by-midpoint: Assign fragments to a nucleosome by nearest midpoint to midpoint in a nucleosome reference
• pipeline/assign-by-edge: Assign fragments to a nucleosome by nearest edge to midpoint in a nucleosome reference. Works independently of fragment edges

Example

Pipeline:

• First create nucleosome references in the directory pipeline/make-nuc-file (read README.md in there)
• Then create fragments from BAM files in the directory pipeline/arr-paired-reads (read README.md in there)
• Then run one of the other pipielines (read README.md in their directories)

Example: create nucleosome reference nuc_fil.tsv. Create fragments in dir frags. Run assign-by-edge, list_all.py frags nuc_fil.tsv out

Contact: Tobias Røikjer, tobias.roikjer@post.au.dk