Skip to content

Latest commit

 

History

History
71 lines (58 loc) · 2.57 KB

Installation_ATAC.md

File metadata and controls

71 lines (58 loc) · 2.57 KB
Raw

Installation Guide for Practical Couse of SOSE 2021 (Part 2)

## Environment: Linux 64 bits
## The tools are tested on Linux Mint 20.1 - Ulyssa, 64bit. and Ubuntu 20.04

1. SRA toolkit

The SRA Toolkit is a collection of tools and libraries for using data in the NCBI Sequence Read Archives. Download the latest software at

https://github.com/ncbi/sra-tools/wiki/01.-Downloading-SRA-Toolkit

And place the binaries in any folder contained in your $PATH. Make sure they are executable (770). See here for more information about installing SRA toolkit.

2. Bowtie 2

Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences, you can install it by

sudo apt install bowtie2

If you are interested in the details, find here the paper.

3. Samtools

Samtools is a suite of programs for interacting with high-throughput sequencing data. We will use it for further processing the aligned data.

sudo apt install samtools

4. MACS2

MACS2 (Model-based Analysis for ChIP-Seq) is a tool for identifying regions with enriched reads. Though this method was originally developed for ChIP-Seq, now it becomes the standard tool for analysis other NGS data, such as ATAC-seq.

pip install --user macs2

5. RGT

RGT is an open source Python 3.6+ library for analysis of regulatory genomics developed by CostaLab. The RGT toolbox is made of a core library and several tools. We will use it to perform motif matching in this tutorial.

pip install RGT

# setup genomic data
cd ~/rgtdata
python setupGenomicData.py --mm10

6. Download Data

We will use publicly available ATAC-seq in this lecture, so please ensure you download them successfully.

First, setup your working directory

mkdir ~/Practice
cd ~/Practice

You can download directly from GEO server by

prefetch SRR1533863 SRR1533847

This could be very slow depending on your internet. In this case, please download the data from our server

wget https://costalab.ukaachen.de/open_data/bioinfolab_2021/practical_atac/SRR1533847.sra --no-check-certificate
wget https://costalab.ukaachen.de/open_data/bioinfolab_2021/practical_atac/SRR1533863.sra --no-check-certificate

Check if the files are complete

md5sum SRR1533847.sra
md5sum SRR1533863.sra

# 9752428b0382a12a4ce83676ef3153d0  SRR1533847.sra
# 7b6d6e0899003adce137c9ea2cd592df  SRR1533863.sra