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)
Usage: ft predict-m6a [OPTIONS] [BAM] [OUT]
Arguments:
[BAM]
Bam HiFi file with kinetics
[default: -]
[OUT]
Output bam file with m6A calls in new/extended MM and ML bam tags
[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]
--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]
-k, --keep
Keep hifi kinetics data
-h, --help
Print help (see a summary with '-h')
-V, --version
Print version
Developer-Options:
-m, --min-ml-score <MIN_ML_SCORE>
Set a minimum ML score to keep on instead of using the model specific minimum ML score
-a, --all-calls
Keep all m6A calls regardless of how low the ML value is
-b, --batch-size <BATCH_SIZE>
Number of reads to include in batch prediction
Increasing improves GPU performance at the cost of memory.
[default: 1]
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