New version of the popular ChIP-Seq caller SICER out.
See https://github.com/biocore-ntnu/epic2 for more.
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] [--example] epic2. (Visit github.com/endrebak/epic2 for examples and help.) optional arguments: -h, --help show this help message and exit --treatment TREATMENT [TREATMENT ...], -t TREATMENT [TREATMENT ...] 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 required. --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). --false-discovery-rate-cutoff FALSE_DISCOVERY_RATE_CUTOFF, -fdr FALSE_DISCOVERY_RATE_CUTOFF Remove all islands with an FDR below cutoff. Default 0.05. --effective-genome-fraction EFFECTIVE_GENOME_FRACTION, -egf EFFECTIVE_GENOME_FRACTION 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 1. --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.