OBDS-Training / pipeline_rnaseq_hisat2

A minimal pipeline demonstrating the processing paired-end RNA-sequencing using cgatcore and HISAT2.

Usage

Setup - Files

Clone this repository.

git clone git@github.com:OBDS-Training/pipeline_rnaseq_hisat2.git

Create sub-directories for the input files.

mkdir data
mkdir data/fastq
mkdir data/hisat2_index

Download an example set of compressed FASTQ files into the data/fastq/ directory.

wget \
  https://github.com/sims-lab/simulated_ngs_datasets/raw/files/human.chr22.genes2/outputs/simulated_reads/sample_01_R1.fastq.gz \
  https://github.com/sims-lab/simulated_ngs_datasets/raw/files/human.chr22.genes2/outputs/simulated_reads/sample_01_R2.fastq.gz \
  https://github.com/sims-lab/simulated_ngs_datasets/raw/files/human.chr22.genes2/outputs/simulated_reads/sample_02_R1.fastq.gz \
  https://github.com/sims-lab/simulated_ngs_datasets/raw/files/human.chr22.genes2/outputs/simulated_reads/sample_02_R2.fastq.gz \
  -P data/fastq \
  --no-verbose

Download an example genome FASTA file into the data/ directory, and decompress it.

wget \
  http://ftp.ensembl.org/pub/release-104/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.chromosome.22.fa.gz \
  -P data \
  --no-verbose
gunzip data/Homo_sapiens.GRCh38.dna.chromosome.22.fa.gz

Download a precomputed HISAT2 index for the example genome FASTA above.

wget \
  https://github.com/sims-lab/simulated_ngs_datasets/raw/files/human.chr22.genes2/outputs/hisat2_chr22.1.ht2 \
  https://github.com/sims-lab/simulated_ngs_datasets/raw/files/human.chr22.genes2/outputs/hisat2_chr22.2.ht2 \
  https://github.com/sims-lab/simulated_ngs_datasets/raw/files/human.chr22.genes2/outputs/hisat2_chr22.3.ht2 \
  https://github.com/sims-lab/simulated_ngs_datasets/raw/files/human.chr22.genes2/outputs/hisat2_chr22.4.ht2 \
  https://github.com/sims-lab/simulated_ngs_datasets/raw/files/human.chr22.genes2/outputs/hisat2_chr22.5.ht2 \
  https://github.com/sims-lab/simulated_ngs_datasets/raw/files/human.chr22.genes2/outputs/hisat2_chr22.6.ht2 \
  https://github.com/sims-lab/simulated_ngs_datasets/raw/files/human.chr22.genes2/outputs/hisat2_chr22.7.ht2 \
  https://github.com/sims-lab/simulated_ngs_datasets/raw/files/human.chr22.genes2/outputs/hisat2_chr22.8.ht2 \
  -P data/hisat2_index \
  --no-verbose

Download an example GTF file into the data/ directory.

wget \
  https://raw.githubusercontent.com/sims-lab/simulated_ngs_datasets/files/human.chr22.genes2/outputs/chr22.genes2.gtf \
  -P data \
  --no-verbose

Setup - Environment

Create the Conda environment expected by the pipeline, using the conda.yml.

mamba env create -f conda.yml

Activate the Conda environment.

conda activate pipeline_rnaseq_hisat2

Execution

Launch the pipeline.

python pipeline.py make full -v 5

The example above request the execution of entire pipeline (make full), with maximal verbosity (-v 5).

Resources

• Learn more about Conda and Mamba in our Conda workshops