macs2_randsample(1)
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