macs2_bdgdiff(1)
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.