This is a project which is currently making use of HPC facilities at Newcastle University. It is active.
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This project investigates the epigenetic regulation of musculoskeletal (MSK) tissues, with a focus on understanding how chromatin architecture, histone modifications, and accessible regulatory elements contribute to tissue function and disease. Using large-scale sequencing datasets such as ATAC-seq, ChIP-seq, Hi-C, Capture-Hi-C, and methylation profiling, we aim to map regulatory variation across cell types relevant to MSK biology. The project involves integrating multiple genomic datasets, comparing disease and control tissue states, and identifying regulatory elements that may influence gene expression or contribute to disease mechanisms. The HPC facility will support the processing, alignment, and analysis of these datasets.
The project will make extensive use of R, Bioconductor, and Python for processing and analysing high-throughput sequencing datasets. Key tools include packages for differential accessibility, peak calling, Hi-C/CHi-C interaction mapping, and statistical integration of multi-omic data. Typical workflows involve alignment, quality control, matrix generation, loop calling, annotation, and visualization of chromatin interactions. Additional software may include samtools, bedtools, HiCUP, CHiCAGO, and other genomics pipelines requiring parallel computation and high-memory nodes. The HPC environment will provide the compute power required to efficiently run these workflows, handle large genomic files, and perform downstream modelling and integrative analyses.