Skip to content

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

Notifications You must be signed in to change notification settings

ferygood/nf-STAR-TEtranscript

Folders and files

NameName
Last commit message
Last commit date

Latest commit

 

History

63 Commits
 
 
 
 
 
 
 
 
 
 

Repository files navigation

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>
  1. 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)

About

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

Topics

Resources

Stars

Watchers

Forks