Tool: New ultraperformant version of SICER/epic: epic2
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11 weeks ago by
endrebak85290 wrote:

New version of the popular ChIP-Seq caller SICER out.

See for more.


enter image description here


usage: epic2 [-h] [--treatment TREATMENT [TREATMENT ...]]
             [--control CONTROL [CONTROL ...]] [--genome GENOME]
             [--keep-duplicates] [--bin-size BIN_SIZE]
             [--gaps-allowed GAPS_ALLOWED] [--fragment-size FRAGMENT_SIZE]
             [--false-discovery-rate-cutoff FALSE_DISCOVERY_RATE_CUTOFF]
             [--effective-genome-fraction EFFECTIVE_GENOME_FRACTION]
             [--chromsizes CHROMSIZES] [--e-value E_VALUE] [--quiet]

epic2. (Visit for examples and help.)

optional arguments:
  -h, --help            show this help message and exit
                        Treatment (pull-down) file(s) in one of these formats:
                        bed, bedpe, bed.gz, bedpe.gz or (single-end) bam, sam.
                        Mixing file formats is allowed.
  --control CONTROL [CONTROL ...], -c CONTROL [CONTROL ...]
                        Control (input) file(s) in one of these formats: bed,
                        bedpe, bed.gz, bedpe.gz or (single-end) bam, sam.
                        Mixing file formats is allowed.
  --genome GENOME, -gn GENOME
                        Which genome to analyze. Default: hg19. If
                        --chromsizes and --egf flag is given, --genome is not
  --keep-duplicates, -kd
                        Keep reads mapping to the same position on the same
                        strand within a library. Default: False.
  --bin-size BIN_SIZE, -bin BIN_SIZE
                        Size of the windows to scan the genome. BIN-SIZE is
                        the smallest possible island. Default 200.
  --gaps-allowed GAPS_ALLOWED, -g GAPS_ALLOWED
                        This number is multiplied by the window size to
                        determine the number of gaps (ineligible windows)
                        allowed between two eligible windows. Must be an
                        integer. Default: 3.
  --fragment-size FRAGMENT_SIZE, -fs FRAGMENT_SIZE
                        (Single end reads only) Size of the sequenced
                        fragment. Each read is extended half the fragment size
                        from the 5' end. Default 150 (i.e. extend by 75).
                        Remove all islands with an FDR below cutoff. Default
                        Use a different effective genome fraction than the one
                        included in epic2. The default value depends on the
                        genome and readlength, but is a number between 0 and
  --chromsizes CHROMSIZES, -cs CHROMSIZES
                        Set the chromosome lengths yourself in a file with two
                        columns: chromosome names and sizes. Useful to analyze
                        custom genomes, assemblies or simulated data. Only
                        chromosomes included in the file will be analyzed.
  --e-value E_VALUE, -e E_VALUE
                        The E-value controls the genome-wide error rate of
                        identified islands under the random background
                        assumption. Should be used when not using a control
                        library. Default: 1000.
  --quiet, -q           Do not write output messages to stderr.
  --example, -ex        Show the paths of the example data and print example command.
tool chip-seq • 249 views
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