wind: wORKFLOW FOR PiRNAs AnD BEYONd

<a href="https://doi.org/10.5281/zenodo.6603418"><img src="https://zenodo.org/badge/DOI/10.5281/zenodo.6603418.svg" alt="DOI"></a>

We have developed a bioinformatics workflow that could reliably characterise sequences from small-RNA sequencing to different databases of small non-coding RNAs, and more precisely tackle the crucial issue regarding the piRNA annotation. You can find the published article here: f1000

The workflow consists of three significant steps:

1. Annotation forging: the generation of the annotation files for small RNA sequences used in the next quantification step.
2. Pre-processing & Quantification: pre-processing, alignment and quantification of the reads assigned to sncRNAs (using a dual approach: genomic and transcriptomic analysis).
3. Exploratory data analysis: result exploration of both quantification methods in parallel and Differential Expression (DE) with two different methodologies (edgeR and limma-voom).

Logo | workflow --- | --- <img src="WIND_LOGO.png" width="600"> | <img src="Figure_workflow.jpg" width="600">