This is the command macs2_randsample 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_randsample - Model-based Analysis for ChIP-Sequencing
DESCRIPTION
usage: macs2 randsample [-h] -t TFILE [TFILE ...] (-p PERCENTAGE | -n NUMBER)
[--seed SEED] [-o OUTPUTFILE] [--outdir OUTDIR]
[-s TSIZE] [-f {AUTO,BAM,SAM,BED,ELAND,ELANDMULTI,ELANDEXPORT,BOWTIE}] [--verbose
VERBOSE]
optional arguments:
-h, --help
show this help message and exit
-t TFILE [TFILE ...], --tfile TFILE [TFILE ...]
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.
-p PERCENTAGE, --percentage PERCENTAGE
Percentage of tags you want to keep. Input 80.0 for 80%. This option can't be used
at the same time with -n/--num. REQUIRED
-n NUMBER, --number NUMBER
Number of tags you want to keep. Input 8000000 or 8e+6 for 8 million. This option
can't be used at the same time with -p/--percent. Note that the number of tags in
output is approximate as the number specified here. REQUIRED
--seed SEED
Set the random seed while down sampling data. Must be a non-negative integer in
order to be effective. DEFAULT: not set
-o OUTPUTFILE, --ofile OUTPUTFILE
Output BED file name. If not specified, will write to standard output. DEFAULT:
stdout
--outdir OUTDIR
If specified all output files will be written to that directory. Default: the
current working directory
-s TSIZE, --tsize TSIZE
Tag size. This will override the auto detected tag size. DEFAULT: Not set
-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 macs2 randsample decide
which format the file is. Please check the definition in README file if you choose
ELAND/ELANDMULTI/ELANDEXPORT/SAM/BAM/BOWTIE. 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
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