Support repository demonstrating the usage of redefine_peaks from glbase3
Two examples are provided from the paper. The CTCF and MED1/MED12 examples.
You require glbase3 to be installed: https://github.com/oaxiom/glbase3
Then run the scripts in this order: MED1/MED12 example: redefine_peaks/med1_med12_example/flats/make_flats.sh # This can take some time, and you only need to complete it once to get the FLAT files redefine_peaks/med1_med12_example/before_redefine/group.py redefine_peaks/med1_med12_example/redefine/redefine.py redefine_peaks/med1_med12_example/after_redefine/group.py
CTCF example: redefine_peaks/ctcf_example/flats/make_flats.sh # This can take some time! and you only need to complete it once to get the FLAT files redefine_peaks/ctcf_example/macs2/pack_finals.py (Optional) redefine_peaks/ctcf_example/before_redefine/group.py redefine_peaks/ctcf_example/redefine/redefine.py redefine_peaks/ctcf_example/after_redefine/group.py