Smart Consensus Of RNA Expression pipelines

1. Setup
2. Usage
3. FAQ
4. License

Download and extract the latest stable release of SCORE from here.

Dependencies:

• Anaconda or Miniconda
• gffutils
• Python 3
• Snakemake (< 4.6.0)

Optional:

• git (Download)
• Graphviz (DAG visualization)
• Sequanix (GUI)

Please ensure that the latest versions of the dependencies listed above are installed on your system.

Then run the installation script:

./libraries/miscellaneous/install.sh

Alternatively, SCORE can be installed via Docker.

Dependencies:

• Docker

Use the following command to install the SCORE docker container:

docker pull eppinglen/score:v1.0.1

Download and edit the SCORE config file:

wget https://github.com/SiWolf/SCORE/blob/master/config.yaml

And run SCORE for your data:

sudo docker run --rm -it -v <your config.yaml>:/SCORE/config.yaml  -v <directory with reads and metadata>:/SCORE/raw -v <references genomes directory>:/SCORE/references -v <output directory>:/SCORE/deg -w /SCORE eppinglen/score:v1.0.1 /bin/bash run-SCORE.sh <amount_of_threads> <PE/SE>

Or for the test data:

sudo docker run --rm -it -v <output directory>:/SCORE/deg -w /SCORE eppinglen/score:v1.0.1 /bin/bash run-SCORE-test.sh <amount_of_threads> <study_number>

Requirements:

• Adapter-Trimmed RNA-Seq Reads (.fastq or .fastq.gz)
• Reference Annotation File (.gff)
• Reference Genome (.fasta)

Place input reads into the raw/ directory and reference files into references/.

Set parameters in the following files:

• config.yaml
• raw/Metadata.tsv

And run SCORE:

./run-SCORE.sh <amount_of_threads> <PE/SE>

For more details please refer to our wiki.

The current version of SCORE includes configuration files for downloading and analyzing a selection of published data sets:

1. Houser, John R., et al. "Controlled measurement and comparative analysis of cellular components in E. coli reveals broad regulatory changes in response to glucose starvation." PLoS computational biology 11.8 (2015).
2. Peyrusson, Frédéric, et al. "Intracellular Staphylococcus aureus persisters upon antibiotic exposure." Nature Communications 11.1 (2020): 1-14.
3. Rodman, Nyah, et al. "Human pleural fluid elicits pyruvate and phenylalanine metabolism in Acinetobacter baumannii to enhance cytotoxicity and immune evasion." Frontiers in microbiology 10 (2019): 1581.

The following command can be used to download the data and run SCORE:

./run-SCORE-test.sh <amount_of_threads> <study_number>

Downloads provided by SRA-Explorer.

How can I compute the total runtime of my analysis?

Using the executable script mentioned above will automatically output the runtime at successful termination. Sequanix will not provide additional runtime information.

I can't edit the config file and I can't use Sequanix, is there another way of setting parameters?

Yes, it is possible to either edit the Snakefile itself (not recommended) or using the command "snakemake -s "SCORE_PE.snk" --config {parameter}={value}" to set a specified {parameter} to a {value}.

Snakemake is unable to activate the included environments - what can I do?

You are possibly using an incompatible version of Conda (> 4.5.13). Conda has underwent several syntax updates since August 2019, resulting in incompatibility with certain Snakemake versions. Following the advice mentioned here, please install Conda version 4.5.13 and modify your .bashrc in order to ensure compability with Snakemake.

# Add the following line to your .bashrc file
# Restart your terminal afterwards
export PATH="/full/path/to/miniconda3/bin:$PATH"

# Install the required conda version
conda install -n base conda=4.5.13

Snakemake outputs an error stating that not all output, log and benchmarking files contain the same wildcards? What does this mean?

Starting with Snakemake version 5 and above, the syntax for dynamic rules has been updated. Please use Snakemake version 4.6.0 for running SCORE.

How do I cite SCORE?

Please cite the following:

Wolf, Silver A., et al. "SCORE: Smart Consensus Of RNA Expression-a consensus tool for detecting differentially expressed genes in bacteria." Bioinformatics (2020). https://doi.org/10.1093/bioinformatics/btaa681.

This project is licensed under the GPLv3 License. See the LICENSE file for more details.