Extract fiberseq data into plain text files.
See https://fiberseq.github.io/fibertools-rs/docs/extract.html for a description of the outputs.
Usage: ft extract [OPTIONS] [BAM]
Arguments:
[BAM]
Input fiberseq bam file. If no path is provided extract will read bam data from stdin
[default: -]
Options:
-r, --reference
Report in reference sequence coordinates
--molecular
Report positions in the molecular sequence coordinates
-m, --min-ml-score <MIN_ML_SCORE>
Minium score in the ML tag to include in the output
[default: 125]
--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 a tabular format including "all" fiberseq information in the bam
-h, --help
Print help (see a summary with '-h')
-V, --version
Print version
All-Format-Options:
-q, --quality
Include per base quality scores in "fiber_qual"
-s, --simplify
Simplify output by remove fiber sequence
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