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macs2_filterdup - Model-based Analysis for ChIP-Sequencing


usage: macs2 filterdup [-h] -i IFILE [IFILE ...]

[-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.

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

-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

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 duplicates in bit 1024, MACS2 will discard them no matter how you set

--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

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

-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

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