trusty (1) filterdup.1.gz

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