.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.16.
.TH MACS2_PREDICTD "1" "December 2020" "macs2 predictd 2.2.7.1" "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] [\-\-d\-min D_MIN]
[\-m MFOLD MFOLD] [\-\-outdir OUTDIR] [\-\-rfile RFILE]
[\-\-buffer\-size BUFFER_SIZE] [\-\-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\-\-d\-min\fR D_MIN
Minimum fragment size in basepair. Any predicted
fragment size less than this will be excluded.
DEFAULT: 20
.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\-\-buffer\-size\fR BUFFER_SIZE
Buffer size for incrementally increasing internal
array size to store reads alignment information. In
most cases, you don't have to change this parameter.
However, if there are large number of
chromosomes/contigs/scaffolds in your alignment, it's
recommended to specify a smaller buffer size in order
to decrease memory usage (but it will take longer time
to read alignment files). Minimum memory requested for
reading an alignment file is about # of CHROMOSOME *
BUFFER_SIZE * 8 Bytes. DEFAULT: 100000
.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