Man page - macs3_bdgdiff(1)

Packages contains this manual

Package:  macs
apt-get install macs

Manuals in package:
• macs3_bdgpeakcall(1)
• macs3_filterdup(1)
• macs3_pileup(1)
• macs3_bdgopt(1)
• macs3_bdgcmp(1)
• macs3_bdgdiff(1)
• macs3_bdgbroadcall(1)
• macs3_callpeak(1)
• macs3(1)
• macs3_randsample(1)
• macs3_refinepeak(1)
• macs3_predictd(1)
• macs3_cmbreps(1)
Documentations in package:
• macs

Manual

MAC3_BDGDIFF

NAME
DESCRIPTION
options:

---

NAME

mac3_bdgdiff - Model-based Analysis for ChIP-Sequencing

DESCRIPTION

usage: macs3 bdgdiff [-h] --t1 T1BDG --t2 T2BDG --c1 C1BDG --c2 C2BDG
[-C CUTOFF] [-l MINLEN] [-g MAXGAP] [--d1 DEPTH1]

[--d2 DEPTH2] [--verbose VERBOSE] [--outdir OUTDIR] ( --o-prefix OPREFIX | -o OFILE OFILE OFILE)

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

log10LR cutoff. Regions with signals lower than cutoff will not be considerred as enriched regions. DEFAULT: 3 (likelihood ratio=1000)

-l , --min-len MINLEN

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

-g , --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

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

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

--verbose VERBOSE

Set verbose level of runtime message. 0: only show critical message, 1: show additional warning message, 2: show process information, 3: show debug messages. DEFAULT:2

--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

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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