RabadanLab / mage-pipeline

MAGE - Multilevel Analysis of Gene Expression

mage-pipeline

Overview

Requirements

• Kallisto : expression quantification

• R

  • packages: tidyverse, jsonlite

• Need to have a config.yaml in your project directory:

rootdir: $HOME/mage-pipeline
projdir: /home/ubuntu/mage-user
metafile: meta.txt
gtffile: /home/ubuntu/mage-user/ref/Macaca_mulatta.Mmul_8.0.1.90.gtf
reffasta: /home/ubuntu/mage-user/ref/Macaca_mulatta.Mmul_8.0.1.cdna.all.fa
refindex: /home/ubuntu/mage-user/ref/Macaca_mulatta.Mmul_8.0.1.cdna.all.kallisto_v0.43.0.idx
kallisto: ~/bin/kallisto_linux-v0.43.0/kallisto

Setup

cd mage-pipeline
source setup.sh

Provide the id for each samples

meta.fastq.txt

src/utils/dir2meta.shi can be used to make the meta file

Quantification

Input for quantification

• GTF file
• Fastq file
• Kallisto index

System requirements

sudo apt-get install libssl-dev           # Install Secure Sockets Layer toolkit
sudo apt install make                     # install make 
sudo apt-get install libcurl4-openssl-dev # Install curl 
sudo apt-get install libxml2-dev          # Instal xml

Installing R

# See https://www.r-bloggers.com/how-to-install-r-on-linux-ubuntu-16-04-xenial-xerus/ for more
sudo echo "deb http://cran.rstudio.com/bin/linux/ubuntu xenial/" | sudo tee -a /etc/apt/sources.list
gpg --keyserver keyserver.ubuntu.com --recv-key E084DAB9
gpg -a --export E084DAB9 | sudo apt-key add -
sudo apt-get update
sudo apt-get install r-base r-base-dev

Installing required R packages

R

in R,
source("requirements.R")

# this will install tidyverse, stan

Installing Kallisto

mkdir -p ~/bin
cd ~/bin
curl -L -O https://github.com/pachterlab/kallisto/releases/download/v0.43.1/kallisto_linux-v0.43.1.tar.gz
tar xzvf kallisto_linux-v0.43.1.tar.gz

Creating a Kallisto index

~/bin/kallisto_linux-v0.43.1/kallisto index --index=Macaca_mulatta.Mmul_8.0.1.cdna.all.idx Macaca_mulatta.Mmul_8.0.1.cdna.all.fa

Installing go

Go packages

go get github.com/urfave/cli
go get gopkg.in/yaml.v2

Implementation notes

mage-quant creates quant.ok in the kallisto output directory to indicate everything run well