🔥 FIRE: Fiber-seq Inferred Regulatory Elements

A Snakemake workflow for calling Fiber-seq Inferred Regulatory Elements (FIREs) on single molecules. For a more detailed description and methods see the docs, or watch my lab meeting on FIRE.

Install

Please install snakemake and all the UCSC Kent utilities. For detailed instructions see the installation README.

Configuring

See the configuration README, the example configuration file, and the example manifest file for configuration options.

Run

We have a run script that executes the FIRE snakemake called fire, and any extra parameters are passed directly to snakemake. For example:

./fire --configfile config/config.yaml

If you want to do a dry run:

./fire --configfile config/config.yaml -n

If you want to execute across a cluster (modify profiles/slurm-executor as needed for distributed execution):

./fire --configfile config/config.yaml --profile profiles/slurm-executor

You can also run snakemake directly, e.g.:

snakemake \
  --configfile config/config.yaml \
  --profile profiles/slurm-executor \
  --local-cores 8 -k

Test data

You can find input data to test against at this url.