Can EPIC call peaks on files without control?
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Entering edit mode
5.6 years ago
ariel.balter ▴ 190

The EPIC peak caller is based on SICER. SICER can attempt to call peaks without a control. Is this possible with EPIC as well? The blind approach didn't work:

$ epic -t treated_A.bed  -gn hg38 -cpu 8 -k KEEP_DUPLICATES > test
usage: epic [-h] --treatment TREATMENT [TREATMENT ...] --control CONTROL
            [CONTROL ...] [--number-cores NUMBER_CORES] [--genome GENOME]
            [--keep-duplicates KEEP_DUPLICATES] [--window-size WINDOW_SIZE]
            [--gaps-allowed GAPS_ALLOWED] [--fragment-size FRAGMENT_SIZE]
            [--false-discovery-rate-cutoff FALSE_DISCOVERY_RATE_CUTOFF]
            [--effective_genome_length EFFECTIVE_GENOME_LENGTH]
            [--store-matrix STORE_MATRIX] [--paired-end] [--version]
epic: error: argument --control/-c is required
sicer epic ChIP-Seq peak-calling • 1.7k views
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Entering edit mode
3.2 years ago
endrebak ▴ 900

epic2 supports this: https://github.com/biocore-ntnu/epic2

It also accepts bam, btw XD

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