This is a project which is currently making use of HPC facilities at Newcastle University. It is active.
For further information about this project, please contact:
This project deals with the study of neuromuscular disorders. We have single nuclei RNA-seq, Spatial transcriptomics (10x Visium), single nuclei ATAC-seq data from different NMDs (Pompe, Duchenne, SMA, ALS, VCP) and healthy controls. These datasets are being analysed by using computational methods.
We require access to Jupyter Notebook and R/RStudio for interactive analysis and visualization of snRNA-seq, snATAC-seq, and spatial transcriptomics data. For command-line workflows, we need FastQC, MultiQC, fastp for quality control, STAR, HISAT2, Salmon for alignment and quantification, and samtools, bedtools, featureCounts for file manipulation and counting. Optional tools for multi-modal analyses include bwa, bowtie2, MACS2, and cellranger/spaceranger. These modules will enable end-to-end pre-processing, analysis, and visualization of our datasets.