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:
RNAseq data analysis. We are experimentally generating RNAseq data from cell lines and mouse models where we have disrupted the expression of RNA binding proteins. We want to then analyse this data using bioinformatics tools to find gene expression pathways and splicing patterns that are under control of these RNA binding proteins. We hope that this data will feed into better understanding of how these RNA binding proteins function during normal health and development as well as in disease.
We will analyse gene expression patterns and splicing patterns using programmes including Salmon, DESEQ, RMATS and SUPPA2. We will align RNAseq reads using HiSat2. We will also analyse and visualise our data using programmes in R such as DESeq2. The technology for running these types of analysis are changing with time, so we will use the most up to date methods as they become available. Our bioinformatics skills are also developing, so that will also impact what software and computer analyses we can do.