Add nucleosomes to a bam file with m6a predictions
Usage: ft add-nucleosomes [OPTIONS] [BAM] [OUT]
Arguments:
[BAM] Bam HiFi file with m6A calls [default: -]
[OUT] Output bam file with nucleosome calls [default: -]
Options:
-n, --nucleosome-length <NUCLEOSOME_LENGTH> Minium nucleosome length [default: 75]
-c, --combined-nucleosome-length <COMBINED_NUCLEOSOME_LENGTH> Minium nucleosome length when combining over a single m6A [default: 100]
-m, --min-distance-added <MIN_DISTANCE_ADDED> Minium distance needed to add to an already existing nuc by crossing an m6a [default: 25]
-d, --distance-from-end <DISTANCE_FROM_END> Minimum distance from the end of a fiber to call a nucleosome or MSP [default: 45]
--min-ml-score <MIN_ML_SCORE> Minium score in the ML tag to use in predicting nucleosomes [default: 125]
-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