DSB_TRIP_protocol

git repository to accompany Schep et al. 2022

dependencies

Before running the pipeline, some dependencies need to be installed. Most of them can be installed using conda, others need to be downloaded from git using a bash script.
In addition SRA toolkit needs to be installed manually:
https://github.com/ncbi/sra-tools/wiki/01.-Downloading-SRA-Toolkit

bash download_dependencies.sh

conda env create -f config/DSB_TRIP_env.yml

example run

Before running your own analysis, you can try an example dataset.

conda activate dsb_trip

bash example.sh -t 10

This runs the pipeline on an example dataset using 10 cores.

After downloading the right data from SRA, the following snakemake command is called:

conda activate dsb_trip

snakemake -j 10 -s src/dsb_trip.snake \
          --configfile config/LBR_example_config.yaml \
          --config indir=example/raw outdir=example/results 

By replacing the --configfile and the --config arguments you can run the pipeline on your own experiment.