sep241peakcalling

Peak calling after CUT&TAG 2for1 deconvolution. We use the positional marginal likelihoods to originate from one of the two channels to identify peaks of high cut likelihood for the respective channels according to CUT&Tag2for1: a modified method for simultaneous profiling of the accessible and silenced regulome in single cells.

By default, channel 1 is assumed to contain narrow, sharp peaks. Channel 2 is assumed to contain broad domains of a more gradually changing signal. The minimum peak size can be controlled by --c1-min-peak-size and --c2-min-peak-size. Additionally, signals can be smoothed through --c1-smooth and --c2-smooth before peak calling to reflect a more gradual change.

usage: sep241peakcalling [-h] [-l LEVEL] [--logfile logfile] [-o out_dir]
                         [--c1-min-peak-size int] [--c2-min-peak-size int]
                         [--c1-smooth float] [--c2-smooth float]
                         [--fraction-in-peaks float]
                         [--fraction-overlap float] [--span int] [--no-check]
                         [--only-check] [--uncorrected] [--force]
                         [--no-progress] [--cores int]
                         [jobdata-file]

jobdata-file

Jobdata with cuts per interval and workchunk ids.

-h, --help

show this help message and exit

-l {DEBUG,INFO,WARNING,ERROR,CRITICAL}, --log {DEBUG,INFO,WARNING,ERROR,CRITICAL}

Set the logging level (default=INFO).

--logfile <logfile>

Write detailed log to this file.

-o <out_dir>, --out <out_dir>

Output directory (default is the directory of the jobdata input file).

--c1-min-peak-size <int>

Minimal number of bases per peak for channel 1 (default=100).

--c2-min-peak-size <int>

Minimal number of bases per peak for channel 2 (default=400).

--c1-smooth <float>

Apply gaussian filter with this standard deviation to channel 1 (default=0).

--c2-smooth <float>

Apply gaussian filter with this standard deviation to channel 2 (default=2000).

--fraction-in-peaks <float>

Fraction of reads that are expected to be in peaks (default=0.5).

--fraction-overlap <float>

If more than this fraction of a peak overlaps with a peak of the other target, then it is considered an overlapping region (default=0.5).

--span <int>

Resolution in number of base pairs (default=10).

--no-check

Do not test for flipped length distributions.

--only-check

Stop after initial checking.

--uncorrected

Do not correct cut ratio estimate with Bayesian prior.

--force

Call peaks even if some results are missing.

--no-progress

Do not show progress.

--cores <int>

Number of CPUs to use for the preparation.