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