.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.40.13.
.TH FILTERDUP "1" "December 2012" "filterdup 2.0.9.1" "User Commands"
.SH NAME
filterdup \- Filter duplicate reads depending on sequencing depth
.SH SYNOPSIS
.B filterdup
\fI<-t file> \fR[\fI-o outputfile\fR] [\fI-g genomesize\fR] [\fIoptions\fR]
.SH DESCRIPTION
filterdup \fB\-\-\fR Filter duplicate reads like in MACS. This script can also be used
to convert ELAND result, ELAND multi, ELAND export, SAM, BAM, BOWTIE map
formats to BED format.
.SH OPTIONS
.TP
\fB\-\-version\fR
show program's version number and exit
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit.
.TP
\fB\-t\fR TFILE
Sequencing alignment file. REQUIRED.
.TP
\fB\-o\fR OUTPUTFILE
Output BED file name. If not specified, will write to
standard output. DEFAULT: stdout
.TP
\fB\-f\fR FORMAT, \fB\-\-format\fR=\fIFORMAT\fR
Format of tag file, "AUTO", "BED" or "ELAND" or
"ELANDMULTI" or "ELANDEXPORT" or "SAM" or "BAM" or
"BOWTIE". The default AUTO option will let %prog
decide which format the file is. Please check the
definition in 00README file if you choose
ELAND/ELANDMULTI/ELANDEXPORT/SAM/BAM/BOWTIE. DEFAULT:
"AUTO"
.TP
\fB\-g\fR GSIZE, \fB\-\-gsize\fR=\fIGSIZE\fR
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=\fITSIZE\fR
Tag size. This will overide the auto detected tag
size. DEFAULT: Not set
.TP
\fB\-p\fR PVALUE, \fB\-\-pvalue\fR=\fIPVALUE\fR
Pvalue cutoff for binomial distribution test.
DEFAULT:1e\-5
.TP
\fB\-\-keep\-dup\fR=\fIKEEPDUPLICATES\fR
It controls the %prog behavior towards duplicate tags
at the exact same location \fB\-\-\fR the same coordination
and the same strand. The default 'auto' option makes
%prog 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. Default: auto
.TP
\fB\-\-verbose\fR=\fIVERBOSE\fR
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