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MACS2_RANDSAMPLE(1) |
User Commands |
MACS2_RANDSAMPLE(1) |
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