Fiber-seq toolkit in rust
Usage: ft [OPTIONS] <COMMAND>
Commands:
predict-m6a Predict m6A positions using HiFi kinetics data and encode the results in the MM and ML bam tags. Also adds nucleosome (nl, ns) and MTase sensitive patches (al, as) [aliases: m6A, m6a]
add-nucleosomes Add nucleosomes to a bam file with m6a predictions
fire Add FIREs (Fiber-seq Inferred Regulatory Elements) to a bam file with m6a predictions
extract Extract fiberseq data into plain text files [aliases: ex, e]
center This command centers fiberseq data around given reference positions. This is useful for making aggregate m6A and CpG observations, as well as visualization of SVs [aliases: c, ct]
footprint Infer footprints from fiberseq data
track-decorators Make decorated bed files for fiberseq data
clear-kinetics Remove HiFi kinetics tags from the input bam file
strip-basemods Strip out select base modifications
help Print this message or the help of the given subcommand(s)
Options:
-h, --help Print help
-V, --version Print version
Global-Options:
-t, --threads <THREADS> Threads [default: 8]
Debug-Options:
-v, --verbose... Logging level [-v: Info, -vv: Debug, -vvv: Trace]
--quiet Turn off all logging