GUAVA : A GUI tool for the Analysis and Visualization of ATAC-seq data

GUAVA is a standalone GUI tool for the processing, analysis, and visualization of ATAC-seq data from raw sequencing reads to ATAC-seq signals. GUAVA can compare ATAC-seq signals from two conditions to identify genomic loci with differentially enriched ATAC-seq signals. Furthermore, GUAVA provides results on gene ontology and pathways analysis. Since using GUAVA requires only several clicks and no learning curve, it will help novice bioinformatics researchers and biologist with minimal computer skills to analyze ATAC-seq data. Therefore, we believe that GUAVA is a powerful and time saving tool for ATAC-seq data analysis. The GUAVA setup contains a script to configure and install dependencies which facilitates the GUAVA installation. GUAVA works on Linux and Mac OS.

This document contains all the information that is required to install and use GUAVA.

GUAVA was developed in Edwin Cheung’s laboratory at the University of Macau.

Quick Start

How to download GUAVA

First download the GUAVA package.

Step 1: Go to the link
Step 2: Click on the Source Code (zip)
Step 3: This will save GUAVA zip package in the downloads folder

Then you will need to open the terminal to complete installation.
Please check the manual to know how to open the terminal.

If the downloaded package is in the folder Downloads, Then type the commands below in the Terminal to move "GUAVA-1.zip" into the home folder and unzip it.

mv ~/Downloads/GUAVA-1.zip ~/
cd ~/
unzip GUAVA-1.zip

NOTE
If you have already unzipped package then remove the '.zip' suffix in the first command and skip the third command.
If you have downloaded and saved GUAVA package in any other folder that Downloads. You will have to use complete path of that folder in above command instead of ~/Downloads/GUAVA-master.zip. To copy path, simply copy the downloaded package and paste it on the terminal.

Installing GUAVA

GUAVA depends on other tools in order to process ATAC-seq data (e.g. Bowtie for alignment). If any of the dependencies are not found on the system, GUAVA will not work properly. Therefore, to help users to install the dependencies, we have written a program called configure.sh, which automatically downloads and installs the dependencies. Please follow the steps given below to run configure.sh.

Run configure.sh

cd ~/GUAVA-1
sh ./configure.sh 

NOTE
This may take 15-20 mins to finish. Also, you will need to press ‘enter’ several times to continue. Additionally, answer all questions with ‘yes’. If you see the message about the ‘Xcode’, choose ‘install’ to continue. Some users may need to repeat step 1-3 in the new terminal if it could not load the ‘conda’.

Error: Anaconda Error

End of the installation, Close the terminal.

How to start GUAVA

GUI version

 java -jar GUAVA.jar

For command line interface

 java -jar GUAVA.jar [options]*

GUAVA manual

To download manual click here

Sample Data

To download sample data Click Here

Anaconda Error: Missing write permissions in

If you encounter error which says "Error: Missing write permissions in:/share/apps/anaconda***",
please follow the commands below to create local Anaconda enviroment.

• Use the command below and replace the text after 'clone=' with your Anaconda path. Check the error to know correct path.

  conda create -n my_root --clone=/share/apps/anaconda2/4.0.0

• use commands below to activate loacal my_root anaconda

  source activate my_root
  conda remove conda-build
  conda remove conda-env
  conda update anaconda

• try to install dependencies again cd ~/GUAVA-1 sh ./configure.sh

System Requirements

• Java 1.8 or latest
• Python version 2.7
• R Version: >= 3.3.2
  

Required bioinformatic tools

• Bowtie
• Bowtie2
• MACS2 version 2.1.1.20160309
• SAMtools Version: 1.3.1
• FastQC
• cutadapt
• bedtools
• bedGraphToBigWig

List of required R Packages

• DESeq2
• ChIPpeakAnno
• GO.db
• KEGG.db
• EnsDb.Hsapiens.v75
• Rsubread
• ggplot2
• TxDb.Hsapiens.UCSC.hg19.knownGene
• TxDb.Mmusculus.UCSC.mm9.knownGene
• TxDb.Mmusculus.UCSC.mm10.knownGene
• org.Hs.eg.db
• org.Mm.eg.db

Support

If you're having any problem, please raise an issue on GitHub.