Computing ChIP-seq coverage of replication timing quantiles - Bash and R scripts

BASH scripts

• process.sh
• process2.sh

Divide the genome into genomic windows of a specified size, calculate the mean replication timing (RT) score (or eigenvector score) for each window, compute the coverage of each ChIP-seq BAM file for each genomic window and generate a table [forR.BL.ok.tab] displaying CHIP-seq coverage per genomic window for the different samples (and removes blacklisted regions and "chrUn|chrEBV|chrY|random|\s.\s"). 

R scripts

• Functions
• TMP-per_RTquantile

-Data import [ forR.BL.ok.tab ]

-Data wrangling

-Conversion of coverage data into Tags per million using toTMP function

-Calculates for each sample ‘Coverage in TPM per RT (or eigenvector) quantile’ using convertToQuantiles function

-Generates a box plot of TMP per RT quantile for all samples

-Saves the sets of box plots as a png file