Current status of EPIC peak caller

Question

[ariel.balter]

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.

[Devon Ryan]

The most recent release is 0.1.20, which is available via pypi. I'll update bioconda now so it has 0.1.20 (if you conda install -c bioconda epic you'll currently get 0.1.17). Regarding 0.1.21, I don't think that's released yet. He (endrebak) was just asking me about using pyBigWig a week or so ago, so I imagine the next release needs a bit of time.

[ariel.balter]

So how come I got V0.1.6?

Oh, and should the -b switch for bed files be active now? I'm getting an error. But I'm also getting a funny version. I installed using bioconda as you showed above.

[Devon Ryan]

TravisCI has been having issues, so the bioconda package was only just updated a few hours ago.

$ conda install -c bioconda epic
$ epic --version
epic 0.1.20

Answer 1

[endrebak]

epic is currently deprecated in favor of epic2. epic2 does not support bigwig creation, but I might add a recipe on how to create the same bigwigs with pyranges. Would only be a few lines of code :)