Calling HPV Integration Fusions in RNA Short-Read Sequencing

Workflow for calling HPV integration fusion sites in short-read RNA sequencing data.

Installation

This will clone the repository. You can run workflow within this directory.

git clone https://github.com/vanessa-porter/callRNAHPVFusions

Dependencies

To run this workflow, you must have snakemake (v6.12.3) and conda. You can install snakemake using this guide. The remaining dependencies will be downloaded automatically within the snakemake workflow.

Input Files

RNA-seq

• RNA alignment (bam file)
• HPV integration sites (txt file)

Set Up Configuration Files

Edit the config files

Example parameters.yaml:

Config files to specify parameters and paths needed for the workflow. The main parameter to include is the genome path and the STAR transcriptome reference directory.

genome_path: /path/to/genome/fasta
transcriptome_path: "/path/to/star/transcriptome/directory"

Example samples.yaml:

Main config file to specify input files.

samples:
    sampleName_1: 
        ont-dna-sites: /path/to/hpv_integration_sites.bed
        rna: /path/to/rnaseq.bam
    sampleName_2: 
        ont-dna-sites: /path/to/hpv_integration_sites.bed
        rna: /path/to/rnaseq.bam

Converting sample paths to yaml file

A text file can be converted to the samples.yaml file using the scripts/samplestoyaml.py script. The tsv file should be tab delimited and have the sample name in the first column, the file type in the second column (ont-dna-sites, rna) and the path in the third column (no header).

scripts/sampletsvtoyaml.py -t samples.txt -o config/samples.yaml

Run Workflow

This is the command to run the workflow with snakemake using conda. The -c parameter can be used to specify maximum number of threads.

snakemake -c 30 --use-conda

Contributors

The contributors of this project are Vanessa Porter