dedup-region's Introduction

dedup-region

Example of a snakemake project

Installation

Download the repository from github

git clone https://github.com/Redmar-van-den-Berg/dedup-region.git

Install and activate the conda environment.

conda env create --file environment.yml
conda activate dedup-region

Settings

There are three levels where configuration options are set, in decreasing order of priority.

Flags passed to snakemake using --config, or in the specified --configfile.
Setting specified in the PEP project configuration, under the key dedup-region
The default settings for the pipeline, as specified in the common.smk file

Supported settings

The following settings are available for the pipeline.

Option	Type	Explanation
umi_trie	Required binary	Compiled version of umi-trie (the tests use a dummy version that is not suitable for real data
gtf file	Required gtf file	http://ftp.ensembl.org/pub/release-106/gtf/homo_sapiens/Homo_sapiens.GRCh38.106.gtf.gz
transcripts	List of transcripts	Must match the `transcript_id` from the gtf file

Tests

You can run the tests that accompany this pipeline with the following commands

# Check if requirements are installed, and run linting on the Snakefile
pytest --kwd --tag sanity

# Test the pipeline settings in dry-run mode
pytest --kwd --tag dry-run

# Test the performance of the pipeline by running on the test data
pytest --kwd --tag integration

Limitations

For transcripts located on the mitochondrion, make sure that you rename the entries in the GTF file to use M instead of MT as chromosome name.
If a transcript has no coverage before deduplication, the remaining coverage after deduplication will be shown as 0%. 0% in the `trasncripts/{transcript}_exons.html graph.

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