Testing the setup

If you would like to test the installation of the RNA-seq workflow, we provide a small example data set. This repository contains paired compressed FASTQ files for four samples from the GSE52778 data set, containing only reads aligning to the first 10M bases of chromosome 1 (in the FASTQ directory). In addition, the directory contains a metadata table with information about the four samples, and a reference directory with two collections of reference files (Gencode v28 and Ensembl v93). To use this data set to test your installation, clone the repository and set the paths to the input files, the metadata file and the reference files properly in the config.yaml file.