Campylobacter jejuni biofilm differential expression analysis (DEA)

This is a repository of Linux commands and R script used for the differential expression analysis of the C. jenuni dataset produced by Manca Volk (ORCID) at Biotechnical Faculty, University of Ljubljana (UNI-LJ BF). Dr Marko Petek, NIB (ORCID) and Manca Volk performed the bioinformatic analysis together. The project was supervised by Dr Špela Baebler, NIB (ORCID) and Dr Anja Klančnik, UNI-LJ BF (ORCID).

Content description

Run following scripts in consecutive order:

• Campy_centrifuge_commands.txt -- taxonomic classification of reads to detect sample contamination
• Campy_STAR_commands.txt -- reference index build and RNA-seq read mapping
• Campy_DEA.R -- differential expression analysis R script

We used pISA-tree research data management system to organise scripts, results and metadata.

Bioinformatic software and packages used

• FastQC
• MultiQC
• Centrifuge
• GFFRead
• STAR
• samtools
• Pavian
• edgeR
• limma

R package versions

R version 4.1.1 (2021-08-10)

• stringr_1.4.0
• edgeR_3.36.0
• limma_3.50.3