Pipeline for processing bulk RNA-seq data from raw .fastq files to read counts.
The pipeline is contained within a single shell script and processes short read paired-end .fastq files from bulk RNA-sequencing and outputs raw read counts (un-normalized).
Currently the script is executed using:
bash RNAseq-pipeline.sh -f /path/to/fastqs -t 32
-f - designates the file path for the fastq files to be processed. This is also used as the main working directory and all output files will exist here.
-t - number of threads to use. Must be integer value. If no input specified, then by default 80% of threads on the system will be used.