Venus

Venus: an efficient Virus infection detection and fusion Site discovery method using single-cell and bulk RNA-seq data

Overview

Parameters

Setup

Clone the repository.

git clone https://github.com/aicb-ZhangLabs/Venus.git

Please set repo_dir to your own downloaded location and out_dir to your own output location for easy copy and pasting when running Venus tutorial.

repo_dir=/srv/disk00/cheyul1/Venus/outputs/22-05-10/Venus
out_dir=/srv/disk00/cheyul1/Venus/outputs/22-05-10/testing

Set up the conda envrionment. Note the spec-file.txt is for Linux platform.

conda create --name venus --file ${repo_dir}/reference_files/venus_spec-file.txt
conda activate venus

One can download the mega-virus.fa file directly from here [link]. Please then move the file into the reference_files directory.

mv mega-virus.fa ${repo_dir}/reference_files/

One should also download the human (vGRCh38) fasta, gtf files from NCBI in addition to the 10X single-cell CB whitelist we will use:

cd ${repo_dir}/reference_files
wget https://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCF_000001405.39_GRCh38.p13/GCF_000001405.39_GRCh38.p13_genomic.fna.gz
gunzip GCF_000001405.39_GRCh38.p13_genomic.fna.gz
wget https://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCF_000001405.39_GRCh38.p13/GCF_000001405.39_GRCh38.p13_genomic.gtf.gz
gunzip GCF_000001405.39_GRCh38.p13_genomic.gtf.gz
wget https://github.com/10XGenomics/cellranger/raw/master/lib/python/cellranger/barcodes/3M-february-2018.txt.gz
gunzip 3M-february-2018.txt.gz

Running with test data

There are two main modules in Venus: Detection and Integration. However, one would need to create mapping indices first prior to running these two modules. The detailed steps to do so is stated below:

• Creating Index [link]
• Detection Module [link]
• Integration Module [link]

The expected outputs are given in the 'test_output' directory of the repository.