CompareTranscriptome | repository of scripts for comparative | Genomics library

For effective data management, we suggest creating a folder structure using the script Section2.1_setup_directory.sh on ATH_GMA folder.
This step covers installation of majority of software applying within this protocol. Section2.2_download_software.sh allows users automatically download and install software. If software is successfully installed, the version information for each tool will be displayed. If errors appear rather than the version information for a tool, the tool needs to be installed manually. The versions of software can be changed with different repository URLs for the software.
In addition to the software from the previous step, we will use R, which is a programing language and environment for statistical data analysis. If R is not installed on a system, it will be had to be installed before moving to next step. In order to determine whether the system has R, users can simply type R into the Terminal. To install R packages for this protocol, we recommend typing commands in a R interactive console rather than running this Rscript in a Terminal. R can be started in a Linux or OSX Terminal by typing R. In this protocol, commands preceded by $ are executed under a Linux Terminal, and commands preceded by > are executed under a R console. All R packages for this protocol will be able to be installed though package installers like Bioconductor except OrthoClust. OrthoClust is required to be installed from its package file, and OrthoClust_1.0.tar.gz is included in software directory of this GitHub repository. Some packages require other packages as their dependencies such as OrthoClust requires igraph. We recommend allowing R Package Installer to install dependences together. This process could take a while and return wordy messages. When a package has been installed successfully, * DONE (PACKAGE NAME) usually appears on a console. The installation process can be verified by typing library('PACKAGE NAME').
The Araport and DOE phytozome database both require free registration to access and download their data. After downloading sequence files and gene annotation files, these files are needed to be moved into the ATH_GMA/raw_data directory to let future scripts to work on these files. Then, compressed *.gz files can be de-compressed with gunzip command such as gunzip [a gz file].
Arabidopsis: Araport web site (www.araport.org) genomic sequences: TAIR10_Chr.all.fasta.gz on https://www.araport.org/downloads/TAIR10_genome_release/assembly protein-coding sequences: Araport11_genes.201606.pep.fasta.gz on https://www.araport.org/downloads/Araport11_latest gene annotation: Araport11_GFF3_genes_transposons.201606.gtf.gz on https://www.araport.org/downloads/Araport11_latest
soybean: DOE phytozome database (https://phytozome.jgi.doe.gov/pz/portal.html#!bulk?org=Org_Gmax) genomic sequences: Gmax_275_v2.0.fa.gz protein-coding sequences: Gmax_275_Wm82.a2.v1.protein.fa.gz gene annotation: Gmax_275_Wm82.a2.v1.gene_exons.gff3.gz
fastq-dump is a tool from the Sequence Read Archive (SRA) toolkit, and allows the user to download raw sequencing data with SRR accession ID from SRA. If fastq-dump is already installed from the 2.2 Software installation section, then typing fastq-dump in a Terminal shows its usage and version information, and it is located in the ATH_GMA/software/sratoolkit.2.8.2-1-centos_linux64/bin/fastq-dump directory. The example below is to download a sequencing file (accession ID: SRR2927328) to the ./raw_data directory. We provide the Section2.5_download_fastq.sh script and two text files with a list of SRR accession IDs (PRJNA301162.txt for Arabidopsis and PRJNA197379.txt for soybean) for allowing easy download with multiple SRR files. Since downloading sped would be various depending on network environments, the approximated execution time can be estimated by running the script with a test file, PRJNAtest.txt. Obtained files will be located in the ATH_GMA/raw_data/fastq/[TEST|ATH|GMA] directory.
After installing the software from the 2.2 Software installation section, we recommend the user either to add paths of the installed software in the bashrc or bash_profile file in the system for continues uses or to export their paths on every use.