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:
The project will involve bioinformatic (e.g. RNA-Seq) and bioimaging (e.g. dSTORM super-resolution microscopy) analysis for PhD projects on antibiotic resistance in Gram-negative bacteria including Pseudomonas aeruginosa, Klebsiella pneumoniae, and Escherichia coli. The workflow will involve processing and analysing sequencing datasets within a Linux HPC environment, including raw sequencing quality assessment, genome alignment, BAM file processing, gene-level read quantification, and downstream differential gene expression analysis. The bioimaging analysis will be involved reconstruction of the acquired imaging data (ND2 file) and statistic analysis of single molecular tracking, clustering, and density.
The main software and tools include:
FastQC and MultiQC for sequencing quality control and summary reporting;
Bowtie2 for alignment of bacterial RNA-seq reads to the P. aeruginosa reference genome;
SAMtools for SAM/BAM conversion, sorting, indexing, and alignment statistics;
featureCounts/Subread for gene-level read counting using genome annotation files;
R and DESeq2 for downstream statistical analysis, differential expression analysis, data normalisation, and visualisation.
The BioApps container https://hpc.researchcomputing.ncl.ac.uk/dokuwiki/doku.php?id=advanced:software:bioapps appears suitable for the planned RNA-seq analysis workflow and software requirements.