macs2_randsample(1) Model-based Analysis for ChIP-Sequencing


usage: macs2 randsample [-h] -t TFILE [TFILE ...] (-p PERCENTAGE | -n NUMBER)
[--seed SEED] [-o OUTPUTFILE] [--outdir OUTDIR]

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.
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
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
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