rna_seq_pipeline

Graphical description

Installation

This code has been successfully tested to run in python 3.8. You can check your python3 version by prompting: python3 -V. Also, you will need pip3 as a package manager.

It is advisable to use a virtual environment to build the project: python3 -m virtualenv mypython

1. Docker

Docker is required tto install and run some of the pipeline components. To intall it you can follow these instructions: (https://docs.docker.com/engine/install/)

2. Install python3 dependencies

pip3 install -r requeriments.txt

Basic usage:

First, change the configuration parameters from config.yaml that handle genome files location

The, you can run the pipeline with the following command python3 rna_seq_pipeline.py --threads <NUM_CPUS> --fastq_dir <FASTQ_DIR> --output_dir <OUTPUT_DIR> -r <hg19/hg38> --config_yaml config.yaml --docker_yaml docker_images.yaml