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>
Arguments:
<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 the strand is indicated in the 6th column of the bed
file. The 4th column will also be checked for the strand but only after the 6th is.
If you include strand information in the 4th (or 6th) column it will orient data
accordingly and use the end position of bed record instead of the start if on the minus
strand. This means that profiles of motifs in both the forward and minus orientation will
align to the same central position.
Options:
-m, --min-ml-score <MIN_ML_SCORE>
Minium score in the ML tag to include in the output
[default: 125]
-d, --dist <DIST>
Set a maximum distance from the start of the motif to keep a feature
-w, --wide
Provide data in wide format, one row per read
-r, --reference
Return relative reference position instead of relative molecular position
-h, --help
Print help (see a summary with '-h')
-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 of all logging