nanoiso 0.1.0

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nanoISO

nanoISO is a Python package for analyzing ONT cDNA sequencing data. It provides a set of modules for identifying new genes and isoforms

Table of Contents

• 1. nanoISO
• 2. Table of Contents
• 3. Overview
• 4. Requirements
• 5. nanoISO modules
  • 5.1. nanoISO gene
  • 5.2. Usage
  • 5.3. nanoISO isoform
  • 5.4. Usage
  • 5.5. nanoISO m6A sites
  • 5.6. Usage
  • 5.7. nanoISO new mRNA
  • 5.8. Usage
• 6. Scripts
  • 6.1. detect5EU.py
  • 6.2. Usage
• 7. Docker
• 8. Conda Environment
• 9. Cite nanoISO

Overview

Requirements

1. Python 3.8+

nanoISO modules

nanoISO gene

test

nohup python ./modifications.py -i ./treat.pass.fq.gz -s Treat.sam -b genes.bed -o test.treat.mod.bed > test.treat.mod.log 2>&1 &
nohup nanoISO detectMod -i ./treat.pass.fq.gz -s Treat.sam -b genes.bed -o test.treat.mod.detectMod.bed > test.treat.mod.detectMod.log 2>&1 &
nohup nanoISO detectMod -i ../input/LPS3/pass.fq.gz -s ../01_map_gene/LPS3_gene.sam -b ../reference/genes/genes.bed -o ./LPS3_modfi.bed &

Usage

nanoISO.py gene -i sample -f genome.cdna.fa -e 0.005 -o gene

nanoISO isoform

Usage

nanoISO.py isoform -i sample -f genome.cdna.fa -e 0.005 -o isoform

nanoISO m6A sites

Usage

nanoISO.py detectm6A -i sample -f genome.cdna.fa -e 0.005 -o m6A

nanoISO new mRNA

Usage

nanoISO.py detectnewmRNA -i sample -f genome.cdna.fa -e 0.005 -o newmRNA

Scripts

We provide a set of standalone scripts for 5EU detection and quantification.

detect5EU.py

This script detects 5' untranslated regions (5EU) from the ONT direct RNA sequencing data.

Usage

python detect5EU.py -i sample.fastq -o 5EU.bed

Docker

If the user has docker installed, the following command can be used to run the pipeline in a docker container:

docker run -v /path/to/data:/data -it nanoISO/nanoISO:latest /bin/bash

Conda Environment

If the user has conda installed, the following command can be used to create a conda environment for nanoISO:

1. Install conda
2. Create a new conda environment: conda create -n nanoISO python=3.6
3. Activate the environment: conda activate nanoISO
4. Install the required packages: conda install -c bioconda minimap2 samtools bedtools flair tombo mines
5. Install the required python packages: pip install pandas numpy scipy sklearn matplotlib seaborn pysam
6. Clone the nanoISO repository: git clone https://github.com/epibiotek/nanoISO.git
7. Run the pipeline: python nanoISO/nanoISO.py gene -i sample -f genome.cdna.fa -e 0.005 -o gene

Cite nanoISO

If you use nanoISO in your research, please cite the following paper: