FIRST-seq Data Analysis Repository

Project Overview

This repository contains the code, data, and manuscript for our study on FIRST-seq. Our approach leverages customised nanopore direct cDNA sequencing to investigate reverse transcriptase fingerprints and determine RNA secondary structures in long read sequencing reads.

Installation

Clone this repository

git clone https://github.com/YOUR-USERNAME/RNA-Nanopore-Analysis.git
cd RNA-Nanopore-Analysis

Set up dependencies

Ensure R and required packages are installed. We use renv for reproducibility.

Install key dependencies manually:

install.packages(c("tidyverse", "ggplot2", "data.table", "Biostrings", "Seurat"))

Ensure the required libraries are installed in python.

python -m venv venv
source venv/bin/activate
pip install -r requirements.txt

Reference Paper

This repo is created for the research paper below:

Oguzhan Begik, Gregor Diensthuber,Ivana Borovska,John S Mattick,Danny Incarnato,Eva Maria Novoa. "FIRST-seq: a nanopore-based cDNA sequencing platform for RNA modification and structure profiling " Under Review

License

This project is licensed under the MIT License

Contact

For questions, please open an issue here.