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Extracting CTCF-binding sites for the chromatin region of interest

This script produces orientation specific CTCF-binding sites for the 25Mb long chromatin regions defined in the txt file.

Output

Two txt files will be produced from this script.

1) list of orientation specific CTCF binding sites

This file contains two columns, with the first one correponding to the polymer bead ID and the second for type of CTCF-binding sites. Four CTCF types are defined.

1 for 5-3 oriented binding sites
2 for 3-5 oriented binding sites
3 for non-binding sites
4 for multiple binding sites with both orientations

2) index file

This file contains two columns that provide the location of nearest 5-3 and 3-5 CTCF binding sites for a given polymer bead respectively.

Usage:

python genCTCFbinding.py --Cell <Celltype> --bindflex <motif_match_flexibility> --cap <CTCF-cohesin_nearest_dist> --chrom <chromosome_id_array>

or default:

python genCTCFbinding.py

Note items in [] are optional. By default is calculating: Gm12878, chromosome 1.

[--Cell] can be selected any one from the following list (case sensitive):

Gm12878
H1hesc
Hela
Hepg2
Huvec
K562

[--bindflex] is the parameter that indicates the region for the motif matching. The default value is set to be 100bp, which means that if a motif is found within 100bp of the binding site, the orientation of the binding site was then assigned based on the DNA sequence of that motif.

[--cap] is the parameter that indicates the requirement for the nearest genomic distance of CTCF with Rad21. The default value is set to be 50bp.

[--chrom] can be any non-repeated subset selected from 1 to 22. The accepted format is:

1 10 19 21

The CTCF-binding sites input to the model is processed based on the NarrowPeak binding profiles and motifs located in this folder. The generated files as the input of modeling are located in the folder: ./[Celltype]/.

The manual would be available by executing:

python genCTCFbinding.py -h