SYNOPSIS

randsample <-t file> [-p percent|-n number] [-o outputfile] [options]

DESCRIPTION

randsample -- Random sample certain number/percentage of tags. Method: 1. Calculate the percentage of tags needed to be kept; 2. For each chromosome, random sample certain percentage of tags.

OPTIONS

--version

show program's version number and exit

-h, --help

show this help message and exit.

-t TFILE

Sequencing alignment file. 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

-o OUTPUTFILE

Output BED file name. If not specified, will write to standard output. DEFAULT: stdout

-s TSIZE, --tsize=TSIZE

Tag size. This will overide the auto detected tag size. DEFAULT: Not set

-f FORMAT, --format=FORMAT

Format of tag file, "AUTO", "BED" or "ELAND" or "ELANDMULTI" or "ELANDEXPORT" or "SAM" or "BAM" or "BOWTIE". The default AUTO option will let %prog decide which format the file is. Please check the definition in 00README 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