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MACS2_PREDICTD(1) |
User Commands |
MACS2_PREDICTD(1) |
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,BEDPE}]
- [-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,BEDPE},
--format
{AUTO,BAM,SAM,BED,ELAND,ELANDMULTI,ELANDEXPORT,BOWTIE,BAMPE,BEDPE}
- Format of tag file, "AUTO", "BED" or "ELAND"
or "ELANDMULTI" or "ELANDEXPORT" or "SAM" or
"BAM" or "BOWTIE" or "BAMPE" or
"BEDPE". 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