RNA-Seq pipeline. riboduct maps sequence reads onto reference genome, counts
reads on annotated transcripts, computes FPKM and FPKM-UQ. Also computes
several metrics for quality control.
riboduct requires conda package manager. To install conda for Linux,
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh
Download and install riboduct. Here you can replace RIBODUCT_ENV with your favorite name.
git clone https://github.com/msfuji/riboduct.git
cd riboduct
bash riboduct.sh install RIBODUCT_ENV
First, download reference genome and gene annotation to anywhere you want.
# I primarily use the human genome (GRCh37).
wget ftp:https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_19/GRCh37.p13.genome.fa.gz
wget ftp:https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_19/gencode.v19.annotation.gtf.gz
# Alternatively, you may use the human genome GRCh38.
# wget ftp:https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_28/GRCh38.p12.genome.fa.gz
# wget ftp:https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_28/gencode.v28.annotation.gtf.gz
# The mouse genome GRCm38 can be also used.
# wget ftp:https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M18/GRCm38.p6.genome.fa.gz
# wget ftp:https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M18/gencode.vM18.annotation.gtf.gz
Make a database directory, and modify config.yaml so that the db_dir
parameter points to the database directory. Also modify two other parameters
(genome_fa_gz, annotation_gtf_gz) for the downloaded files of genome and
gene annotation. Start indexing of database.
conda activate RIBODUCT_ENV
bash riboduct.sh index config.yaml
conda deactivate
Make a local copy of pipeline for each project.
git clone https://github.com/msfuji/riboduct.git
cd riboduct
Modify config.yaml. First, add path of FASTQ files you want to analyze.
Also modify db_dir to point the directory where you installed database.
When finished, start running the pipeline.
conda activate RIBODUCT_ENV
bash riboduct.sh run config.yaml
conda deactivate