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MACS2_BDGDIFF(1) User Commands MACS2_BDGDIFF(1)

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)

options:

show this help message and exit
MACS pileup bedGraph for condition 1. Incompatible with callpeak --SPMR output. REQUIRED
MACS pileup bedGraph for condition 2. Incompatible with callpeak --SPMR output. REQUIRED
MACS control lambda bedGraph for condition 1. Incompatible with callpeak --SPMR output. REQUIRED
MACS control lambda bedGraph for condition 2. Incompatible with callpeak --SPMR output. REQUIRED
logLR cutoff. DEFAULT: 3 (likelihood ratio=1000)
Minimum length of differential region. Try bigger value to remove small regions. DEFAULT: 200
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
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
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
If specified all output files will be written to that directory. Default: the current working directory
Output file prefix. Actual files will be named as PREFIX_cond1.bed, PREFIX_cond2.bed and PREFIX_common.bed. Mutually exclusive with -o/--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.
December 2023 macs2 bdgdiff 2.2.9.1