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 will analyse of RNA-seq data on cells treated with steroid hormones, or drugs that inhibit their signalling. Specifically, the project will look at RNA levels and RNA processing after treatment. Furthermore, it will analyse ChIP-seq data for hormone receptor chromatin binding from public databases like GEO.
RNA-seq data will be analysed using standard pipelines for differential gene expression (e.g. salmon, hisat2, samtools) plus rMATS for differential splicing analyses. Some datasets will be downloaded from GEO using sra-tools. ChIP-seq data will be downloaded from GEO as well, and then analysed using standard pipelines (e.g. bowtie2, macs2, bedtools).