Tutorial: multi strain

Tutorial for multi-strain bacterial RNA-Seq

Here we will describe a stepwise tutorial on preparing a reference and using bacpipe to process RNA-Seq experiments.

Installation

Clone the repo, install dependencies with conda.

Download the required files

• Reference strains - download Genbank GFF and FNA;
• Our strains - download genome assemblies;
• RNA-Seq reads - download them too.

Setting up working directory

• Make sure there's 50 Gb of space, and it's writable.
• Inside the the working directory you've chosen, create the following dirs: fastqs, study_strains, ref_strains
• Place things appropriately

Prepare reference

• Convert NCBI-style GFFs to Roary-friendly version
• Run prepare_bacterial_reference

Run the pipeline

• Run it! Run it real good!