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.

I just need the FIRE elements

If you only need FIRE elements in the BAM file and don't need the peak-calls or trackHubs that are part of the FIRE pipeline you can do a simplified run FIRE using only ft. e.g.:

# add FIREs to the BAM file
ft fire input.bam fire.bam
# Extract the FIREs from the BAM file into bed format
ft fire --extract fire.bam fire.bed.gz
# if you want the NUC calls and non-FIRE MSPs as well
ft fire --extract --all fire.bam all.bed.gz