This is the command macs2_predictd 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_predictd - Model-based Analysis for ChIP-Sequencing
DESCRIPTION
usage: macs2 predictd [-h] -i IFILE [IFILE ...]
[-f {AUTO,BAM,SAM,BED,ELAND,ELANDMULTI,ELANDEXPORT,BOWTIE,BAMPE}]
[-g GSIZE] [-s TSIZE] [--bw BW] [-m MFOLD MFOLD] [--outdir OUTDIR] [--rfile RFILE]
[--verbose VERBOSE]
optional arguments:
-h, --help
show this help message and exit
-i IFILE [IFILE ...], --ifile IFILE [IFILE ...]
ChIP-seq alignment file. If multiple files are given as '-t A B C', then they will
all be read and combined. Note that pair-end data is not supposed to work with this
command. REQUIRED.
-f {AUTO,BAM,SAM,BED,ELAND,ELANDMULTI,ELANDEXPORT,BOWTIE,BAMPE}, --format
{AUTO,BAM,SAM,BED,ELAND,ELANDMULTI,ELANDEXPORT,BOWTIE,BAMPE}
Format of tag file, "AUTO", "BED" or "ELAND" or "ELANDMULTI" or "ELANDEXPORT" or
"SAM" or "BAM" or "BOWTIE". The default AUTO option will let MACS decide which
format the file is. Please check the definition in README file if you choose
ELAND/ELANDMULTI/ELANDEXPORT/SAM/BAM/BOWTIE. DEFAULT: "AUTO"
-g GSIZE, --gsize GSIZE
Effective genome size. It can be 1.0e+9 or 1000000000, or shortcuts:'hs' for human
(2.7e9), 'mm' for mouse (1.87e9), 'ce' for C. elegans (9e7) and 'dm' for fruitfly
(1.2e8), Default:hs
-s TSIZE, --tsize TSIZE
Tag size. This will override the auto detected tag size. DEFAULT: Not set
--bw BW
Band width for picking regions to compute fragment size. This value is only used
while building the shifting model. DEFAULT: 300
-m MFOLD MFOLD, --mfold MFOLD MFOLD
Select the regions within MFOLD range of highconfidence enrichment ratio against
background to build model. Fold-enrichment in regions must be lower than upper
limit, and higher than the lower limit. Use as "-m 10 30". DEFAULT:5 50
--outdir OUTDIR
If specified all output files will be written to that directory. Default: the
current working directory
--rfile RFILE
PREFIX of filename of R script for drawing X-correlation figure. DEFAULT:'predictd'
and R file will be predicted_model.R
--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
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