emanuelsoda / nf-star-tetranscript

This project aims to develop an nf-core nextflow pipeline to conduct genes and transposable elements from RNA-seq data

nf-STAR-TEtranscript

Introduction

This pipeline is built using Nextflow. The purpose is to handle RNA-seq fastq file from aligning using STAR and estiamte their transposable elements expression using TEtranscript.

Quick Start

1. Install Nextflow (>= 21.10.6)
2. We recommend using this pipeline with Singularity.
3. Downlaod the pipeline and test it with built-in example dataset:

nextflow run nf-core/star-tetranscript -profile test,YOURPROFILE --outdir <OUTDIR>

4. Start running your analysis:

Documentation.

The nf-core pipeline comes with documentation about the pipeline usage, parameters and output.

Credits

Contributions and Supports

References

• Nextflow enables reproducible computational workflows (DOI: 10.1038/nbt.3820)
• STAR: ultrafast universal RNA-seq aligner (DOI: 10.1093/bioinformatics/bts635)
• TEtranscripts: a package for including transposable elements in differential expression analysis of RNA-seq datasets (DOI: 10.1093/bioinformatics/btv422)