RNAseq analysis pipeline for analysis of Illumina short-read sequencing data from Candida auris. This script is used in the Kuchler lab (http://cdl.univie.ac.at/) at MFPL (https://www.mfpl.ac.at/de.html).
C. auris genome sequence and annotation file (obtained from NCBI) are provided. For current version see NCBI.
samtools (http://www.htslib.org/)
FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
MultiQC (https://multiqc.info/)
cutadapt (https://cutadapt.readthedocs.io/en/stable/)
NextGenMap (https://github.com/Cibiv/NextGenMap/wiki)
DeepTools (https://deeptools.readthedocs.io/en/develop/)
HTSeq (https://htseq.readthedocs.io/en/release_0.11.1/#)
All the above-mentioned tools have to be included in yout PATH environment.
Clone the repository by typing "git clone https://github.com/tschemic/RNAseq_analysis_Cauris.git" and copy the raw data into the RNAseq_analysis directory.
Clone the repository and add the read files in the base directory.
Change the adapter sequence for read trimming in the analysis_script.sh file if necessary. By default it contains the Illumina TrueSeq adapter.
Change into the required_files directory and run the analysis script (by typing: bash analysis_script.sh).
After the pipeline has finished change into the diff_expr_analysis directory and use the edgeR_analysis.R script as a basis for differential expression analysis in R.
The blast_analysis.sh script creates a BLAST database from C. albicans protein fasta sequences and performs BLASTp with all C. auris proteins supplied in fasta format on this database to find homologues. A results file (text and excel) is included in the repository (blast.result, Ortho.xlsx).