EnglishFrenchSpanish

Ad


OnWorks favicon

macs2_filterdup - Online in the Cloud

Run macs2_filterdup in OnWorks free hosting provider over Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

This is the command macs2_filterdup that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

NAME


macs2_filterdup - Model-based Analysis for ChIP-Sequencing

DESCRIPTION


usage: macs2 filterdup [-h] -i IFILE [IFILE ...]

[-f {AUTO,BAM,SAM,BED,ELAND,ELANDMULTI,ELANDEXPORT,BOWTIE}]
[-g GSIZE] [-s TSIZE] [-p PVALUE] [--keep-dup KEEPDUPLICATES] [--verbose VERBOSE]
[--outdir OUTDIR] [-o OUTPUTFILE] [-d]

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}, --format
{AUTO,BAM,SAM,BED,ELAND,ELANDMULTI,ELANDEXPORT,BOWTIE}
Format of tag file, "AUTO", "BED" or "ELAND" or "ELANDMULTI" or "ELANDEXPORT" or
"SAM" or "BAM" or "BOWTIE". The default AUTO option will let 'macs2 filterdup'
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

-p PVALUE, --pvalue PVALUE
Pvalue cutoff for binomial distribution test. DEFAULT:1e-5

--keep-dup KEEPDUPLICATES
It controls the 'macs2 filterdup' behavior towards duplicate tags/pairs at the
exact same location -- the same coordination and the same strand. The 'auto' option
makes 'macs2 filterdup' calculate the maximum tags at the exact same location based
on binomal distribution using given -p 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, MACS2 callpeak
function uses KEEPDUPLICATES=1 as default. Note, if you've used samtools or picard
to flag duplicates in bit 1024, MACS2 will discard them no matter how you set
KEEPDUPLICATES. Default: auto

--verbose 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

--outdir OUTDIR
If specified all output files will be written to that directory. Default: the
current working directory

-o OUTPUTFILE, --ofile OUTPUTFILE
Output BED file name. If not specified, will write to standard output. DEFAULT:
stdout

-d, --dry-run
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

Use macs2_filterdup online using onworks.net services


Free Servers & Workstations

Download Windows & Linux apps

  • 1
    NSIS: Nullsoft Scriptable Install System
    NSIS: Nullsoft Scriptable Install System
    NSIS (Nullsoft Scriptable Install
    System) is a professional open source
    system to create Windows installers. It
    is designed to be as small and flexible
    as possi...
    Download NSIS: Nullsoft Scriptable Install System
  • 2
    authpass
    authpass
    AuthPass is an open source password
    manager with support for the popular and
    proven Keepass (kdbx 3.x AND kdbx 4.x ...
    Download authpass
  • 3
    Zabbix
    Zabbix
    Zabbix is an enterprise-class open
    source distributed monitoring solution
    designed to monitor and track
    performance and availability of network
    servers, device...
    Download Zabbix
  • 4
    KDiff3
    KDiff3
    This repository is no longer maintained
    and is kept for archival purposes. See
    https://invent.kde.org/sdk/kdiff3 for
    the newest code and
    https://download.kde.o...
    Download KDiff3
  • 5
    USBLoaderGX
    USBLoaderGX
    USBLoaderGX is a GUI for
    Waninkoko's USB Loader, based on
    libwiigui. It allows listing and
    launching Wii games, Gamecube games and
    homebrew on Wii and WiiU...
    Download USBLoaderGX
  • 6
    Firebird
    Firebird
    Firebird RDBMS offers ANSI SQL features
    & runs on Linux, Windows &
    several Unix platforms. Features
    excellent concurrency & performance
    & power...
    Download Firebird
  • More »

Linux commands

Ad