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:<br>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)<br>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<br>Differentially methylated regions (DMRs): scripts which identify DMRs within MeDIP-seq data<br>Differentially expressed genes (DEGs) and exons (DEEs): scripts responsible for counting number of reads in genes and exons, and determining DEGs and DEEs<br><br>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)<br>