This repository contains scripts used to process and visualise ChIP-seq, Hi-C and RNA-seq data from platypus (Ornithorynchus anatinus).
ChIP-seq data processing scripts available here include those for read trimming (Trimmomatic), read mapping to a reference genome (Subread), and ChIP peak calling (macs2).
ChIP-seq data visualisation/analysis scripts available here include those for intersecting ChIP data with transcription start site (TSS) information, generating TSS metagene plots, calculating ChIP peak densities and performing non-parametric statistical tests.
Hi-C data processing scripts available here include those for read trimming (Trimmomatic), reference genome indexing (bwa), read mapping to a reference genome (bwa) and Hi-C matrix construction and processing (HiCExplorer).
Hi-C data visualisation/analysis scripts available here include those for generating distance-dependent Hi-C contact plots, counting intra- and inter-chromosomal interactions, generating inter-chromosomal interaction plots and generating a top ten chromosome pair plot.
Note: if there is a disparity in the quality of the data, an appropriate subset may be taken to be used in comparative analyses.
RNA-seq data processing scripts available here include those for reference genome indexing (Subread), read mapping to a reference genome (Subread) and feautre counting (Subread).
RNA-seq visualisation/analysis script is for processing, normalising and visualising gene count data.