fibertools-rs

fibertools-rs a CLI tool for interacting with fiberseq bam files.

ft extract

Extracts fiberseq data from a bam file into plain text. ```bash ft-extract 0.0.4 Extract fiberseq data into plain text files

USAGE: ft extract [OPTIONS] [BAM]

ARGS: fiberseq bam file [default: -]

OPTIONS: -r, --reference report in reference sequence coordinates --m6a Output path for m6a bed12 -c, --cpg Output path for 5mC (CpG, primrose) bed12 --msp Output path for methylation sensitive patch (msp) bed12 -n, --nuc Output path for nucleosome bed12 -a, --all Output path for -h, --help Print help information -V, --version Print version information ```

ft-center

Center a fiberseq reads (bam) around a reference position(s). ```bash ft-center 0.0.4 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

USAGE: ft center [OPTIONS]

ARGS: fiberseq bam file, must be aligned and have an index Bed file on which to center fiberseq reads. Data is adjusted to the start position of the bed file and corrected for strand if a 4th strand column is included

OPTIONS: -w, --wide Provide data in wide format, one row per read -h, --help Print help information -V, --version Print version information ```