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