This snakemake workflow runs differential expression analysis from RNA-Seq raw reads through to the plotting of differentially expressed genes. This includes:

• Initial read quality assessment

• Read quality trimming

• Followup quality assessment

• Read alignment to reference

• Generation of count data

• Saturation Curves + PCA plots

• Handles high and low abundance counts

• Volcano plots

• Means to further investigate genes of interest

Requirements

Software

• A Snakemake installation of version ? or higher

• Conda installation

Data

• Compressed Reference genome (fasta file with extension .fna.gz or .fa.gz)

• Associated annotation file (.gff or .gtf extension)

• Compressed paired end illumina reads (extension fastq.gz or fq.gz)

Setup

Get your reads/fastq data

Copy or place all of your fastq data into the 0_data/fastq/ directory. Data can be moved from one location to another using the mv command (example below moves a file called file.fq.gz from its current location to a folder called /newspot)

mv file.fq.gz newspot/

Populate the config file