ATAC-seq

Pipeline for analysing ATAC-seq data from raw fastq files to called genomic peaks

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Table of Contents

1. Overview
2. Pipeline Stages
   • Set up Conda Environment
   • Quality Control
   • Mapping
   • Peak Calling
   • Results
3. How to Run
4. Results

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Overview

Pipeline Stages

Set up Conda Environment

Load the yml file

conda env create -f atacseq.yml

Quality Control

Run FastQC

fastqc -t 8 *fastq.gz -o ./fastqc_initial

Run MultiQC

cd ./fastqc_initial/
multiqc .
firefox multiqc_report.html

Trim Reads

cd ../trimming
./trim-reads-paired.sh

Run FastQC on Trimmed Reads

fastqc -t 8 *fq.gz -o fastqc_trimming/
cd ./fastqc_trimming/
multiqc .
firefox multiqc_report.html

Mapping

Index Reference Genome

Download index files from https://benlangmead.github.io/aws-indexes/bowtie and add them to the mapping folder.

cd ../../../mapping

Run Bowtie2 Alignment

./bowtie2-mapping-paired.sh

Convert SAM to BAM, Sort, and Index BAM

./sam-to-bam.sh

Peak Calling

Mark Duplicates and Filter

cd ../peak_call
./filter.sh

Use MACS2 to Call Peaks

./peak_call.sh

Open IGV and View Peaks

igv

In the IGV GUI choose file > Load from File

How To Run

Results