Question: Can EPIC call peaks on files without control?
gravatar for ariel.balter
3.4 years ago by
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
sicer peak-calling chip-seq epic • 1.1k views
ADD COMMENTlink modified 11 months ago by endrebak810 • written 3.4 years ago by ariel.balter140
gravatar for endrebak
11 months ago by
endrebak810 wrote:

epic2 supports this:

It also accepts bam, btw XD

ADD COMMENTlink written 11 months ago by endrebak810
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 689 users visited in the last hour