NAME

       filterdup - Filter duplicate reads depending on sequencing depth

SYNOPSIS

       filterdup <-t file> [-o outputfile] [-g genomesize] [options]

DESCRIPTION

       filterdup  -- Filter duplicate reads like in MACS. This script can also be used to convert
       ELAND result, ELAND multi, ELAND export, SAM, BAM, BOWTIE map formats to BED format.

OPTIONS

       --version
              show program's version number and exit

       -h, --help
              show this help message and exit.

       -t TFILE
              Sequencing alignment file. REQUIRED.

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

       -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"

       -g GSIZE, --gsize=GSIZE
              Effective genome size. It can be 1.0e+9 or 1000000000, or shortcuts:'hs' for  human
              (2.7e9),  'mm'  for mouse (1.87e9), 'ce' for C. elegans (9e7) and 'dm' for fruitfly
              (1.2e8), DEFAULT:hs

       -s TSIZE, --tsize=TSIZE
              Tag size. This will overide the auto detected tag size. DEFAULT: Not set

       -p PVALUE, --pvalue=PVALUE
              Pvalue cutoff for binomial distribution test.  DEFAULT:1e-5

       --keep-dup=KEEPDUPLICATES
              It controls the %prog behavior towards duplicate tags at the exact same location --
              the  same  coordination  and the same strand. The default 'auto' option makes %prog
              calculate the maximum tags at the exact same location based on binomal distribution
              using  given  -p as pvalue cutoff; and the 'all' option keeps every tags (useful if
              you only want to convert formats). If an integer is given, at most this  number  of
              tags will be kept at the same location. 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