This script processes the output from ChromHMM to extract chromatin states for the 25Mb long chromatin regions defined in the txt file.
A two column txt file will be produced, with the first column indicates the polymer bead ID and the second for chromatin state ID.
python genChromState.py --Cell <Celltype> --chrom <chromosome_id_array>
or default:
python genChromState.py
Note items in [] are optional. By default is calculating: Gm12878, chromosome 1.
[--Cell] can be selected from the following list (case sensitive):
Gm12878
H1hesc
Hela
Hepg2
Huvec
K562
[--chrom] can be any non-repeated subset selected from 1 to 22. The accepted format is:
1 10 19 21
The manual would be available by executing:
python genChromState.py -h