WORK IN PROGRESS

While working with RNAswarm, you might fing bugs, some are known, while others remain undiscovered. We encourage the community to contribute by reporting any issues they encounter on GitHub. Feel free to reach out to me via email or open an issue directly. It's important to note that I cannot be held responsible for any results obtained using RNAswarm or any conclusions drawn from them.

RNAswarm

RNAswarm is a tool for analyzing SPLASH data. It is a Nextflow pipeline that: - Trims (with fastp) and maps (with segemehl) chimeric reads to a reference genome. - Generate heatmaps of interactions between viral segments or/and host transcripts. - Compare groups or mutants to identify differentially structured regions (with DESeq2) - Generate circos plots of potential interactions and potential differentially structured regions.

Dependencies and installation

The pipeline is written in Nextflow, which can be used on any POSIX compatible system (Linux, OS X, etc). Windows system is supported through WSL2. You need Nextflow installed, conda and apptainer. 1. Install Nextflow 2. Install miniconda 3. Install apptainer (from our experience, installing from the pre-built binaries is the easiest way to go) 4. With nextflow installed, you only have to run the pipeline, if you would like to cache the pipeline without running it you can use the following command: bash nextflow pull rnajena/RNAswarm

In the future, only either conda or apptainer will be needed.

Test your installation

This command retrieves the project from GitHub and executes the pipeline using the included test data. It utilizes the default test profile, which employs the provided sample sheet and comparisons sheet, both located in the data/ directory.

bash nextflow run rnajena/RNAswarm \ -profile test,apptainer \ --output <OUTDIR>

Update RNAswarm to the latest version

After you nextflow run, the pipeline is cached by Nextflow. To update to the latest version, you can run the following command: bash nextflow pull rnajena/RNAswarm

Usage

RNAswarm takes as input a sample sheet and a comparisons sheet. The sample sheet contains the information about the samples to be analyzed, while the comparisons sheet contains the groups to be compared.

Creating a sample sheet

Create a sample sheet file with the following columns:

csv sample01,sample01.fastq,reference01.fasta,group01 sample02,sample02.fastq,reference01.fasta,group01 sample03,sample03.fastq,reference02.fasta,group02 sample04,sample04.fastq,reference02.fasta,group02 sample05,sample05.fastq,reference03.fasta,group03 sample06,sample06.fastq,reference03.fasta,group03

Creating a comparisons sheet

Create a comparisons sheet file with the groups for differential analysis: csv group01,group02 group01,group03 group02,group03

Running the pipeline

with local executor

bash nextflow run rnajena/RNAswarm \ -profile local,apptainer \ --samples <SAMPLES_CSV_FILE> \ --comparisons <COMPARISONS_CSV_FILE> \ --output <OUTDIR> \

with slurm

bash nextflow run rnajena/RNAswarm \ -profile slurm,apptainer \ --slurm_queue <SLURM_QUEU_AVAILABLE> \ --samples <SAMPLES_CSV_FILE> \ --comparisons <COMPARISONS_CSV_FILE> \ --output <OUTDIR> \

Cite us

If you use RNAswarm for your analysis, please cite our github repository.

bibtex @software{Lencioni_Lovate_RNAswarm, author = {Lencioni Lovate, Gabriel and Lamkiewicz, Kevin}, license = {MIT}, title = {{RNAswarm}}, url = {https://github.com/rnajena/RNAswarm} }