ft fire

This command identifies Fiber-seq Inferred Regulatory Elements (FIREs) from a Fiber-seq BAM. The input is a Fiber-seq BAM file with m6A and nucleosome calls and the output is a Fiber-seq bam file with the FIREs encoded in the aq tags.

This command can be run in isolation; however, it is usually preferable to run the FIRE pipeline, which runs ft fire and performs many additional analyses and visualizations.

The help page.

Extracting from a FIRE BAM

ft fire can also be used as an extraction tool to extract Fiber-seq data from an already processed FIRE BAM file.

ft fire --extract fire.bam > all.bed

This produces a file in BED format that contains all the MSPs, FIREs, and nucleosomes in the FIRE BAM file. This command produces output analogous to the now removed model.results.bed.gz result from older versions of FIRE pipeline.