Question: Can EPIC call peaks on files without control?
0
gravatar for ariel.balter
2.4 years ago by
ariel.balter140
ariel.balter140 wrote:

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
ADD COMMENTlink modified 8 days ago by endrebak740 • written 2.4 years ago by ariel.balter140
0
gravatar for endrebak
8 days ago by
endrebak740
endrebak740 wrote:

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

It also accepts bam, btw XD

ADD COMMENTlink written 8 days ago by endrebak740
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