schic 0.1.2

scHi-C analysis package

scHIC

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

Overview

Requirements

1. Python 3.8+

scHIC modules

scHIC 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 scHIC 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 scHIC detectMod -i ../input/LPS3/pass.fq.gz -s ../01_map_gene/LPS3_gene.sam -b ../reference/genes/genes.bed -o ./LPS3_modfi.bed &

Usage

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

scHIC isoform

Usage

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

scHIC m6A sites

Usage

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

scHIC new mRNA

Usage

scHIC.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 scHIC/scHIC:latest /bin/bash

Conda Environment

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

1. Install conda
2. Create a new conda environment: conda create -n scHIC python=3.6
3. Activate the environment: conda activate scHIC
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 scHIC repository: git clone https://github.com/epibiotek/scHIC.git
7. Run the pipeline: python scHIC/scHIC.py gene -i sample -f genome.cdna.fa -e 0.005 -o gene

Cite scHIC

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