Processing of dual RNA-seq data for the PhageExpressionAtlas

This repo contains the code for processing dual RNA-seq data as currently hosted in the PhageExpressionAtlas (LINK). First, a nextflow pipeline is used to trim paired-end or single-end RNA-seq reads, check their quality, map the reads to a dual genome, filter the alignments and count reads. A Jupyter Notebook is then used to annotate pre-process the count data for storage and analysis with the PhageExpressionAtlas.

Nextflow pipeline

Tools in the pipeline

Installation & usage

Input & parameters

Output

Pre-processing with the Juypter notebook

Steps

Output

Customization of workflow

Contributing to the PhageExpressionAtlas

References & Acknowledgements