Getting Started

First - ‘Preparing Your Account’ and ‘Miniconda’ installation instructions. All the necessary information about the pipeline is in https://github.com/BleekerLab/snakemake_rnaseq.

• Go to your personal directory

cd ~/personal

• Download the preprocessing pipeline from github

git clone https://github.com/BleekerLab/snakemake_rnaseq

• Go to snakemake folder

cd snakemake_rnaseq/

Installation

Install mamba to install the environment faster (than using conda) .. code-block:: shell

conda install -c conda-forge mamba

Create the environment .. code-block:: shell

mamba env create –name rnaseq –file environment.yaml

To adjust the pipeline to your experiment, you need to modify some parameters.

For this you can either use a text editor for example gedit or you can download it using an ssh client like Filezilla and open it on your own machine.

The former is recommended. If you do the latter, make sure to upload the modified file and replace it.

• Reference Genome and Annotation gtf files

In the ‘config/refs’ folder, add the reference genome and the annotation file of your choice. Then change the name of the files in the ‘config.yaml’ file, adding the path to it. eg.:

refs:
    genome:  "config/refs/hg38.analysisSet.fa"
    gtf:     "config/refs/gencode.v37.annotation.gtf"

• Sample file

Make sure to replace the example config/samples.tsv file with the one relevant to your own experiment. This should include at least 3 columns: sample, fq1 and fq2.