options:

-h, --help

show this help message and exit

--t1 T1BDG

MACS pileup bedGraph for condition 1. Incompatible with callpeak --SPMR output. REQUIRED

--t2 T2BDG

MACS pileup bedGraph for condition 2. Incompatible with callpeak --SPMR output. REQUIRED

--c1 C1BDG

MACS control lambda bedGraph for condition 1. Incompatible with callpeak --SPMR output. REQUIRED

--c2 C2BDG

MACS control lambda bedGraph for condition 2. Incompatible with callpeak --SPMR output. REQUIRED

-C CUTOFF, --cutoff CUTOFF

logLR cutoff. DEFAULT: 3 (likelihood ratio=1000)

-l MINLEN, --min-len MINLEN

Minimum length of differential region. Try bigger value to remove small regions. DEFAULT: 200

-g MAXGAP, --max-gap MAXGAP

Maximum gap to merge nearby differential regions. Consider a wider gap for broad marks. Maximum gap should be smaller than minimum length (-g). DEFAULT: 100

--d1 DEPTH1, --depth1 DEPTH1

Sequencing depth (# of non-redundant reads in million) for condition 1. It will be used together with --d2. See description for --d2 below for how to assign them. Default: 1

--d2 DEPTH2, --depth2 DEPTH2

Sequencing depth (# of non-redundant reads in million) for condition 2. It will be used together with --d1. DEPTH1 and DEPTH2 will be used to calculate scaling factor for each sample, to down-scale larger sample to the level of smaller one. For example, while comparing 10 million condition 1 and 20 million condition 2, use --d1 10 --d2 20, then pileup value in bedGraph for condition 2 will be divided by 2. Default: 1

--outdir OUTDIR

If specified all output files will be written to that directory. Default: the current working directory

--o-prefix OPREFIX

Output file prefix. Actual files will be named as PREFIX_cond1.bed, PREFIX_cond2.bed and PREFIX_common.bed. Mutually exclusive with -o/--ofile.

-o OFILE OFILE OFILE, --ofile OFILE OFILE OFILE

Output filenames. Must give three arguments in order: 1. file for unique regions in condition 1; 2. file for unique regions in condition 2; 3. file for common regions in both conditions. Note: mutually exclusive with --o-prefix.