Home - MeryemAk/dRNASeq GitHub Wiki

Welcome to the dRNASeq wiki!

What is dRNASeq?

dual RNA sequencing (dRNASeq) analysis is designed to enable researchers to identify differentially expressed genes in both the host and pathogen at the same time. The host in this project is the Homo sapiens and the pathogens are yeast cells causing vulvovaginal candidiasis and bacteria causing bacterial vaginosis. The data used in this pipeline are vaginal swabs sequencing through Nanopore sequencing.

Getting Started

This GitHub repository contains two ways of executing the pipeline. 1) A fully automated Nextflow script within Docker or 2) Individual scripts that have to be executed manually within a Conda environment.

Explore the Documentation for Nextflow:
* Installation of Docker: Learn how to install Docker on your system.
* Usage of Nextflow script: Find detailed instructions and examples on how to run the Nextflow pipeline.
* Standard Operating Procedure for Nextflow: Discover practical use cases and step-by-step tutorials demonstrating the Nextflow script.

Explore the Documentation for the scripts:
* Installation of Conda: Learn how to install Conda on your system and set up the Conda environment.
* Usage of scripts: Find detailed instructions and examples on how to run the scripts.
* Standard Operating Procedure for scripts: Discover practical use cases and step-by-step tutorials demonstrating the scripts.

Requirements:
* Kraken database: Before running the script, download the Kraken database.
* Build Docker images: A few Docker images need to be built on the system locally.