usage: macs2 filterdup [-h] -i IFILE [IFILE ...]
[-f {AUTO,BAM,SAM,BED,ELAND,ELANDMULTI,ELANDEXPORT,BOWTIE,BAMPE,BEDPE}]
[-g GSIZE] [-s TSIZE] [-p PVALUE] [--keep-dup KEEPDUPLICATES] [--buffer-size BUFFER_SIZE]
[--verbose VERBOSE] [--outdir OUTDIR] [-o OUTPUTFILE] [-d]
options:-h, --help
show this help message and exit
-i IFILE [IFILE ...], --ifile IFILE [IFILE ...]
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,BAMPE,BEDPE}, --format
{AUTO,BAM,SAM,BED,ELAND,ELANDMULTI,ELANDEXPORT,BOWTIE,BAMPE,BEDPE}
Format of tag file, "AUTO", "BED" or "ELAND" or "ELANDMULTI" or "ELANDEXPORT" or "SAM" or "BAM" or
"BOWTIE" or "BAMPE" or "BEDPE". 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 or BAMPE/BEDPE. 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
--buffer-size BUFFER_SIZE
Buffer size for incrementally increasing internal array size to store reads alignment information.
In most cases, you don't have to change this parameter. However, if there are large number of
chromosomes/contigs/scaffolds in your alignment, it's recommended to specify a smaller buffer size
in order to decrease memory usage (but it will take longer time to read alignment files). Minimum
memory requested for reading an alignment file is about # of CHROMOSOME * BUFFER_SIZE * 8 Bytes.
DEFAULT: 100000
--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. Note, if the input format
is BAMPE or BEDPE, the output will be in BEDPE format. 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
macs2 filterdup 2.2.7.1 April 2022 MACS2_FILTERDUP(1)
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