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PROGRAM:

NAME


macs2_bdgdiff - Model-based Analysis for ChIP-Sequencing

DESCRIPTION


usage: macs2 bdgdiff [-h] --t1 T1BDG --t2 T2BDG --c1 C1BDG --c2 C2BDG

[-C CUTOFF] [-l MINLEN] [-g MAXGAP] [--d1 DEPTH1]
[--d2 DEPTH2] [--outdir OUTDIR] (--o-prefix OPREFIX | -o OFILE OFILE OFILE)

optional arguments:
-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.

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