.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.4.
.TH MACS2_PREDICTD "1" "May 2016" "macs2_predictd 2.1.1.20160309" "User Commands"
.SH NAME
macs2_predictd \- Model\-based Analysis for ChIP\-Sequencing
.SH DESCRIPTION
usage: macs2 predictd [\-h] \fB\-i\fR IFILE [IFILE ...]
.TP
[\-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]
.SS "optional arguments:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-i\fR IFILE [IFILE ...], \fB\-\-ifile\fR 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.
.TP
\fB\-f\fR {AUTO,BAM,SAM,BED,ELAND,ELANDMULTI,ELANDEXPORT,BOWTIE,BAMPE,BEDPE}, \fB\-\-format\fR {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"
.TP
\fB\-g\fR GSIZE, \fB\-\-gsize\fR 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
.TP
\fB\-s\fR TSIZE, \fB\-\-tsize\fR TSIZE
Tag size. This will override the auto detected tag
size. DEFAULT: Not set
.TP
\fB\-\-bw\fR BW
Band width for picking regions to compute fragment
size. This value is only used while building the
shifting model. DEFAULT: 300
.TP
\fB\-m\fR MFOLD MFOLD, \fB\-\-mfold\fR 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
.TP
\fB\-\-outdir\fR OUTDIR
If specified all output files will be written to that
directory. Default: the current working directory
.TP
\fB\-\-rfile\fR RFILE
PREFIX of filename of R script for drawing
X\-correlation figure. DEFAULT:'predictd' and R file
will be predicted_model.R
.TP
\fB\-\-verbose\fR 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