TRF2-DNase-ChIP

Codes for data processing and figure generation

R packages

install.packages(c("progess","plyr","ggplot2"))

python modules used

import numpy 
import matplotlib
import seaborn
import scipy
import pybedtools
import pysam
import json
import pandas
import re
import collections
import itertools
import tables

Download ENCODE DNase files

• Download and store the DNase file using the meta file information.

Rscript 1-a-download-DNase-ENCODE.R

• Rename DNase files

Rscript 1-b-recode-DNase.R

• Download hg19 chromosome length file

Rscript 1-c-hg19-information.R

Compute DES per chromosome

• DES in TRF2 vs Random

python 2-b-Figure-2A.py

Figure-2A

• DES per chromosome comparison

Rscript 2-c-Suppl-Figure-2.R

Supplementary figure-2

• DES differences between TRF2 and Random

python 2-d-Figure-2B-TRF2vsRandom.py

Figure-2B

Histones marks overlap with TRF2

• Download Histone peaks from ENCODE

Rscript 3-a-download-ENCODE-Histone-marks.R

• Find closest mark

python 3-b-histones-closest-dist.py

• Format histone file names

Rscript 3-c-format-filename-histone-marks.R

• Generate Figure 2A-C and supplementary figure 4A-D

python 3-d-generate-Fig-3A-C-and-Suppl-fig-4A-D.py

Figure-3A

Figure-3B and Figure-3C