Genome-wide chromatin and gene expression profiling during memory formation and maintenance in adult mice. [CODE: scripts]

This repository contains the shell, R and python scripts used to generate 4 different analyses: Pre-processing: scripts responsible for generating of alignment files for downstream analyses, merging of said alignment files, generating of bigWig files for data visualisation and various Quality Control (QC) Differential histone post-translational modifications (DHPTMs): scripts which estimate shift sizes and peaks from ChIP-seq data, and identify DHPTMs in peaks, transcription start site (TSS) regions and gene bodies Differentially methylated regions (DMRs): scripts which identify DMRs within MeDIP-seq data Differentially expressed genes (DEGs) and exons (DEEs): scripts responsible for counting number of reads in genes and exons, and determining DEGs and DEEs The complete details on how to run the various scripts are included in the file run_scientific_data_analysis.pdf, which shows how to run all analyses with the aid of reference files (https://dx.doi.org/10.6084/m9.figshare.3487679) and demo samples (https://dx.doi.org/10.6084/m9.figshare.3487391)