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MACS2_FILTERDUP(1) |
User Commands |
MACS2_FILTERDUP(1) |
NAME¶
macs2_filterdup - Model-based Analysis for ChIP-Sequencing
DESCRIPTION¶
usage: macs2 filterdup [-h] -i IFILE [IFILE ...]
- [-f {AUTO,BAM,SAM,BED,ELAND,ELANDMULTI,ELANDEXPORT,BOWTIE}]
- [-g GSIZE] [-s TSIZE] [-p PVALUE] [--keep-dup KEEPDUPLICATES] [--verbose
VERBOSE] [--outdir OUTDIR] [-o OUTPUTFILE] [-d]
optional arguments:¶
- -h, --help
- show this help message and exit
- -i IFILE [IFILE ...], --ifile IFILE [IFILE ...]
- ChIP-seq alignment file. If multiple files are given as '-t A B C', then
they will all be read and combined. Note that pair-end data is not
supposed to work with this command. REQUIRED.
- -f {AUTO,BAM,SAM,BED,ELAND,ELANDMULTI,ELANDEXPORT,BOWTIE},
--format {AUTO,BAM,SAM,BED,ELAND,ELANDMULTI,ELANDEXPORT,BOWTIE}
- Format of tag file, "AUTO", "BED" or "ELAND"
or "ELANDMULTI" or "ELANDEXPORT" or "SAM" or
"BAM" or "BOWTIE". The default AUTO option will let
'macs2 filterdup' decide which format the file is. Please check the
definition in README 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 override 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 'macs2 filterdup' behavior towards duplicate tags/pairs at
the exact same location -- the same coordination and the same
strand. The 'auto' option makes 'macs2 filterdup' 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. Note, MACS2 callpeak
function uses KEEPDUPLICATES=1 as default. Note, if you've used samtools
or picard to flag reads as 'PCR/Optical duplicate' in bit 1024, MACS2 will
still read them although the reads may be decided by MACS2 as duplicate
later. 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
- --outdir OUTDIR
- If specified all output files will be written to that directory. Default:
the current working directory
- -o OUTPUTFILE, --ofile OUTPUTFILE
- Output BED file name. If not specified, will write to standard output.
DEFAULT: stdout
- -d, --dry-run
- When set, filterdup will only output numbers instead of writing output
files, including maximum allowable duplicates, total number of reads
before filtering, total number of reads after filtering, and redundant
rate. Default: not set