What is the status of the options for the epic peak caller? The most recent version in the changelog is v0.1.2 (unreleased). I just installed it with conda and it brought down 0.1.6.
(p2) bicb199:examples balter$ epic --version epic 0.1.6
Also, the changelogs for 0.1.19 removed all bedgraph and bigwig options, but they are still on the README docs.
0.1.20 says that there is a new
-b option for creating bed files (as output I assume), but I get an error that that option is not recognized, so maybe it has been removed?
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: unrecognized arguments: -b
0.1.21 says that it uses
pyBigWig to create bigwigs, but I'm not sure how to use this functionality.