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.

ft-extract 0.0.4
Extract fiberseq data into plain text files

USAGE:
    ft extract [OPTIONS] [BAM]

ARGS:
    <BAM>    fiberseq bam file [default: -]

OPTIONS:
    -r, --reference    report in reference sequence coordinates
        --m6a <M6A>    Output path for m6a bed12
    -c, --cpg <CPG>    Output path for 5mC (CpG, primrose) bed12
        --msp <MSP>    Output path for methylation sensitive patch (msp) bed12
    -n, --nuc <NUC>    Output path for nucleosome bed12
    -a, --all <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).

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] <BAM> <BED>

ARGS:
    <BAM>    fiberseq bam file, must be aligned and have an index
    <BED>    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