.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
.TH MAC3_FILTERDUP "1" "February 2024" "macs3 filterdup 3.0.1" "User Commands"
.SH NAME
mac3_filterdup \- Model\-based Analysis for ChIP\-Sequencing
.SH DESCRIPTION
usage: macs3 filterdup [\-h] \fB\-i\fR IFILE [IFILE ...]
.TP
[\-f {AUTO,BAM,SAM,BED,ELAND,ELANDMULTI,ELANDEXPORT,BOWTIE,BAMPE,BEDPE}]
[\-g GSIZE] [\-s TSIZE] [\-p PVALUE]
[\-\-keep\-dup KEEPDUPLICATES] [\-\-buffer\-size BUFFER_SIZE]
[\-\-verbose VERBOSE] [\-\-outdir OUTDIR] [\-o OUTPUTFILE]
[\-d]
.SS "options:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-i\fR IFILE [IFILE ...], \fB\-\-ifile\fR IFILE [IFILE ...]
Alignment file. If multiple files are given as '\-t A B
C', then they will all be read and combined. 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 'macs3 filterdup' decide which format
the file is. Please check the definition in README
file if you choose
ELAND/ELANDMULTI/ELANDEXPORT/SAM/BAM/BOWTIE or
BAMPE/BEDPE. 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 (2,913,022,398), 'mm' for
mouse (2,652,783,500), 'ce' for C. elegans
(100,286,401) and 'dm' for fruitfly (142,573,017),
Default:hs. The effective genome size numbers for the
above four species are collected from Deeptools https:
//deeptools.readthedocs.io/en/develop/content/feature/
effectiveGenomeSize.html Please refer to deeptools to
define the best genome size you plan to use.
.TP
\fB\-s\fR TSIZE, \fB\-\-tsize\fR TSIZE
Tag size. This will override the auto detected tag
size. DEFAULT: Not set
.TP
\fB\-p\fR PVALUE, \fB\-\-pvalue\fR PVALUE
Pvalue cutoff for binomial distribution test.
DEFAULT:1e\-5
.TP
\fB\-\-keep\-dup\fR KEEPDUPLICATES
It controls the 'macs3 filterdup' behavior towards
duplicate tags/pairs at the exact same location \fB\-\-\fR the
same coordination and the same strand. The 'auto'
option makes 'macs3 filterdup' calculate the maximum
tags at the exact same location based on binomal
distribution using given \fB\-p\fR as pvalue cutoff; and the
\&'all' option keeps every tags (useful if you only want
to convert formats). If an integer is given, at most
this number of tags will be kept at the same location.
Note, MACS3 callpeak function uses KEEPDUPLICATES=1 as
default. Note, if you've used samtools or picard to
flag reads as 'PCR/Optical duplicate' in bit 1024,
MACS3 will still read them although the reads may be
decided by MACS3 as duplicate later. Default: auto
.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. 0: only show critical message, 1:
show additional warning message, 2: show process
information, 3: show debug messages. If you want to
know where are the duplicate reads, use 3. DEFAULT:2
.TP
\fB\-\-outdir\fR OUTDIR
If specified all output files will be written to that
directory. Default: the current working directory
.TP
\fB\-o\fR OUTPUTFILE, \fB\-\-ofile\fR OUTPUTFILE
Output BED file name. If not specified, will write to
standard output. Note, if the input format is BAMPE or
BEDPE, the output will be in BEDPE format. DEFAULT:
stdout
.TP
\fB\-d\fR, \fB\-\-dry\-run\fR
When set, filterdup will only output numbers instead
of writing output files, including maximum allowable
duplicates, total number of reads before filtering,
total number of reads after filtering, and redundant
rate. Default: not set