Examples
Analyze a subset variants in the yeast genome
1. Download the yeast genome and variants
First, change directories to where you would like your test files to be located. Then create a folder titled “yeast_data”
mkdir yeast_data
Next, download the yeast genome and gene file from Ensembl.
wget http://ftp.ensemblgenomes.org/pub/fungi/release-55/fasta/saccharomyces_cerevisiae/dna/Saccharomyces_cerevisiae.R64-1-1.dna.toplevel.fa.gz
wget https://ftp.ensembl.org/pub/release-109/gff3/saccharomyces_cerevisiae/Saccharomyces_cerevisiae.R64-1-1.109.gff3.gz
Unzip the files and move them to the yeast_data folder
gunzip Saccharomyces_cerevisiae.R64-1-1.dna.toplevel.fa.gz && mv Saccharomyces_cerevisiae.R64-1-1.dna.toplevel.fa yeast_data/
gunzip Saccharomyces_cerevisiae.R64-1-1.109.gff3.gz && mv Saccharomyces_cerevisiae.R64-1-1.109.gff3 yeast_data/
Next, download the variants from Ensembl. We will just use a small subset of the variants for this example.
wget http://ftp.ensemblgenomes.org/pub/fungi/release-55/variation/vcf/saccharomyces_cerevisiae/saccharomyces_cerevisiae.vcf.gz
gunzip saccharomyces_cerevisiae.vcf.gz && mv saccharomyces_cerevisiae.vcf yeast_data/
head -n 1000 yeast_data/saccharomyces_cerevisiae.vcf > yeast_data/saccharomyces_cerevisiae.1000.vcf
rm yeast_data/saccharomyces_cerevisiae.vcf
2. Run the SPARCS pipeline
We will use the config file located in the SPARCS/test_files directory.
First, change directories to the SPARCS folder. Then, copy the config file to the workflow folder using the following commands:
cd yeast_data
sparcs --vcf saccharomyces_cerevisiae.1000.vcf --ref-genome Saccharomyces_cerevisiae.R64-1-1.dna.toplevel.fa --gff Saccharomyces_cerevisiae.R64-1-1.109.gff3
cd sparcs_pipeline
bash sparcs.sh
You should see a folder in your working directory called sparcs_pipeline with the following files: - logs - results - temp
- The results folder contains the following files:
combined_ribosnitch_predictions_37.txtcombined_ribosnitch_prediction_hist_37.0.png
