NAME¶
randsample - Random sample certain number/percentage of tags
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