.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.16.
.TH MACS2_BDGDIFF "1" "December 2020" "macs2 bdgdiff 2.2.7.1" "User Commands"
.SH NAME
macs2_bdgdiff \- Model\-based Analysis for ChIP\-Sequencing
.SH DESCRIPTION
usage: macs2 bdgdiff [\-h] \fB\-\-t1\fR T1BDG \fB\-\-t2\fR T2BDG \fB\-\-c1\fR C1BDG \fB\-\-c2\fR C2BDG
.TP
[\-C CUTOFF] [\-l MINLEN] [\-g MAXGAP] [\-\-d1 DEPTH1]
[\-\-d2 DEPTH2] [\-\-outdir OUTDIR]
(\fB\-\-o\-prefix\fR OPREFIX | \fB\-o\fR OFILE OFILE OFILE)
.SS "optional arguments:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-\-t1\fR T1BDG
MACS pileup bedGraph for condition 1. Incompatible
with callpeak \fB\-\-SPMR\fR output. REQUIRED
.TP
\fB\-\-t2\fR T2BDG
MACS pileup bedGraph for condition 2. Incompatible
with callpeak \fB\-\-SPMR\fR output. REQUIRED
.TP
\fB\-\-c1\fR C1BDG
MACS control lambda bedGraph for condition 1.
Incompatible with callpeak \fB\-\-SPMR\fR output. REQUIRED
.TP
\fB\-\-c2\fR C2BDG
MACS control lambda bedGraph for condition 2.
Incompatible with callpeak \fB\-\-SPMR\fR output. REQUIRED
.TP
\fB\-C\fR CUTOFF, \fB\-\-cutoff\fR CUTOFF
logLR cutoff. DEFAULT: 3 (likelihood ratio=1000)
.TP
\fB\-l\fR MINLEN, \fB\-\-min\-len\fR MINLEN
Minimum length of differential region. Try bigger
value to remove small regions. DEFAULT: 200
.TP
\fB\-g\fR MAXGAP, \fB\-\-max\-gap\fR MAXGAP
Maximum gap to merge nearby differential regions.
Consider a wider gap for broad marks. Maximum gap
should be smaller than minimum length (\fB\-g\fR). DEFAULT:
100
.TP
\fB\-\-d1\fR DEPTH1, \fB\-\-depth1\fR DEPTH1
Sequencing depth (# of non\-redundant reads in million)
for condition 1. It will be used together with \fB\-\-d2\fR.
See description for \fB\-\-d2\fR below for how to assign them.
Default: 1
.TP
\fB\-\-d2\fR DEPTH2, \fB\-\-depth2\fR DEPTH2
Sequencing depth (# of non\-redundant reads in million)
for condition 2. It will be used together with \fB\-\-d1\fR.
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
\fB\-\-d1\fR 10 \fB\-\-d2\fR 20, then pileup value in bedGraph for
condition 2 will be divided by 2. Default: 1
.TP
\fB\-\-outdir\fR OUTDIR
If specified all output files will be written to that
directory. Default: the current working directory
.TP
\fB\-\-o\-prefix\fR OPREFIX
Output file prefix. Actual files will be named as
PREFIX_cond1.bed, PREFIX_cond2.bed and
PREFIX_common.bed. Mutually exclusive with \fB\-o\fR/\-\-ofile.
.TP
\fB\-o\fR OFILE OFILE OFILE, \fB\-\-ofile\fR 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 \fB\-\-o\-prefix\fR.