options:¶

-h, --help

show this help message and exit

-i IFILE [IFILE ...], --ifile IFILE [IFILE ...]

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. Note, if the input format is BAMPE or BEDPE, the output will be in BEDPE format. 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,BAMPE,BEDPE}, --format {AUTO,BAM,SAM,BED,ELAND,ELANDMULTI,ELANDEXPORT,BOWTIE,BAMPE,BEDPE}

Format of tag file, "AUTO", "BED" or "ELAND" or "ELANDMULTI" or "ELANDEXPORT" or "SAM" or "BAM" or "BOWTIE" or "BAMPE" or "BEDPE". 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 or BAMPE/BEDPE. DEFAULT: "AUTO"

--buffer-size BUFFER_SIZE

Buffer size for incrementally increasing internal array size to store reads alignment information. In most cases, you don't have to change this parameter. However, if there are large number of chromosomes/contigs/scaffolds in your alignment, it's recommended to specify a smaller buffer size in order to decrease memory usage (but it will take longer time to read alignment files). Minimum memory requested for reading an alignment file is about # of CHROMOSOME * BUFFER_SIZE * 8 Bytes. DEFAULT: 100000

--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