🔥 FIRE: Fiber-seq Inferred Regulatory Elements

A Snakemake workflow for calling Fiber-seq Inferred Regulatory Elements (FIREs) on single molecules.

Configuring

See config/config.yaml and config/config.tbl for configuration options.

Install

You will need snakemake and all the UCSC Kent utilities and the latest version of them (v455).

Add a snakemake conda prefix to your bashrc, e.g. in the Stergachis lab add:

export SNAKEMAKE_CONDA_PREFIX=/mmfs1/gscratch/stergachislab/snakemake-conda-envs

Then snakemake installs all the additional requirements as conda envs in that directory.

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/compute as needed for distributed execution):

./fire --configfile config/config.yaml --profile profiles/compute

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

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

Outputs

Directory	File	Description
coverage
	{all,hap1,hap2}_element_coverages.bed.gz	Coverage tracks for FIREs, nucleosomes, and linkers
	exclude-from-shuffles.bed.gz	Regions to exclude when making null distributions
	{sample}.{bed.gz,d4}	bedgraph of coverages
	{sample}.{median, maximum,minimum}.coverage.txt	Allowed coverage range for analysis
fiber-calls
	FIRE.bed.gz	Every FIRE element in every FIRE
	model.results.bed.gz	Every FIRE, linker, and nucleosome in every fiber
	fire-fibers.bed.gz	bed12 start and end of every fiber
	fire-fiber-decorators.bed.gz	decorator file that adds annotations of FIRE elements to the bed12 file
FDR-peaks
	FDR-FIRE-peaks.bed.gz	Fiber-seq peak calls
	FDR-wide-peaks.bed.gz	Fiber-seq wide peak calls
	FDR.track.bed.gz	Track of FDR significance of accessibility
	{sm}.peaks-vs-percent.pdf	Number of peaks vs % accessible
all/hap1/hap2
	percent.accessible.bed.gz	% of (haplotype) fibers that are accessible
hap1-vs-hap2
	FIRE.hap.differences.bed	Large table of FIREs that are different between hap1 and hap2
	hap1-vs-hap2-volcano.pdf	Volcano plot of FIREs that are different between hap1 and hap2
	hap1-vs-hap2.pdf	Scatter plot of FIREs and their percent accessibility for each hap
trackHub
	*	a trackHub directory that can be loaded into the UCSC browser

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Test data

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