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macs2_bdgdiff - Online in the Cloud

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This is the command macs2_bdgdiff that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

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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