Package: peako
PeaKOWhat is peaKO?PeaKO discovers motifs in ChIP-seq datasets with knockout controls. PeaKO takes in paired wild-type/knockout BAM files in addition to several reference files, as input. It returns a file of ranked motifs (seeour paperfor more details).Quick startDependenciesConda (Miniconda or Anaconda)MEME Suite version 5.1.0 or MEME Suite version 4.12.0 with our CentriMo binary* (see below)Please note that Conda can be installed locally without system administrator privileges. We suggest followingMiniconda's installation instructions.
PeaKO has only been tested on Linux systems.InstallationDownload peaKO'senvironmentfile.Open a terminal and runconda env create -f peako-env.ymlin your Downloads directory. This will create a Conda environment called "peako".Runconda activate peakoorsource activate peakoto activate this environment.Install peaKO from PyPI by runningpython3 -m pip install peako.You can test that this worked by runningpeako --help.NOTES:If you run into errors indicating missing bs4 or pyYAML packages, try runningpip3 install beautifulsoup4==4.8.2 pyyaml.
If step 2 above fails to create a Conda environment, you may try:conda create --name peakoconda activate peako  # or source activate peakoconda install python=3.7conda install -c anaconda beautifulsoup4=4.7 pandasconda install -c bioconda -c conda-forge -c anaconda snakemake-minimal flake8 pathlib2 ipython twineconda install -c bioconda pybedtoolsPlease note that we have only tested peaKO on Linux.Instructions for our modified CentriMo binaryIf MEME Suite version 5.1.0 is installed on your system and accessible in your path, you do not need to install our CentriMo binary separately.
Important: MEME Suite 5.1.0 must be installed from source and should not be installed from Conda at this time due to documented implementation issues.
Future versions of peaKO will support installation of MEME Suite through Conda once these issues are resolved.
If you are using an older version of MEME Suite, please follow the steps below to replace the CentriMo binary with our own to use peaKO.Download MEME distribution 4.12.0 from theMEME Suite Download page.Follow the "Quick Install" steps on theMEME Suite Installation pageup untilmake install.After runningmake install, replace$HOME/meme/bin/centrimowith ourmodified CentriMo binary.Make sure that$HOME/meme/binis located on your$PATH. You should now be able to callcentrimo --help.UsagePeaKO uses Snakemake, which is a workflow management system.
You can run peaKO either locally or on a compute cluster using the Slurm job scheduling system.
To run on Slurm, you must create your owncluster.configfile (template) and provide it to peaKO via--sm-cluster-config.Each step of the workflow either inherits from the main activated Conda environment ("peako") or uses its own separate environment.
If you are working on a compute cluster, run peaKO first with--sm-build-envson a node with internet access to create these additional Conda environments.
Then, you can run it on the cluster without internet, providing a Slurm configuration file (see above).After activating peaKO's Conda environment (conda activate peakoorsource activate peako), you can run peako as follows:peako <outdir> <wt-bam> <ko-bam> <organism> <chr-sizes> <trf-masked-genome> <motif-database> [options]There are 7 required arguments. Please provide absolute paths for files and directories.outdir: output directory (please make sure this already exists); all output directories and files will be created herewt-bam: wild-type sample BAM fileko-bam: knockout sample BAM fileorganism: name of organism (must be eithermouseorhuman)chr-sizes: chromosome sizes file of reference genome (TXT)trf-masked-genome: TRF masked reference genome file (FASTA)motif-database: JASPAR motif database (MEME)Here are the optional arguments:General:-hor--help: access the help message and exit-Vor--version: show the program's version and exitPeaKO submodule:-j <JASPAR_ID>: transcription factor motif JASPAR identifier (e.g. MA0083.3)-m <MOTIF>: transcription factor motif common name (e.g. SRF)--extra: output all intermediate peaKO files for plotting--pickle: use pickled peaKO dictionaries from previous runSnakemake:--sm-build-envs: build conda environments for workflow and exit (requires internet connection)--sm-cluster-config: snakemake cluster configuration file (JSON)OutputCurrently, peaKO generates output directories and files for each step.
These can all be found under your providedoutdirdirectory.
PeaKO's main output file is<outdir>/peako_out/peaKO-rankings.txt, which contains a ranked list of motifs.Additional resourcesSource code is available at:https://github.com/hoffmangroup/peako.We have deposited thecurrent version of the code,example HTML and TXT CentriMo outputs, and amodified CentriMo binaryon Zenodo.CitationIf you found peaKO useful, please cite:Denisko D, Viner C, Hoffman MM. Motif elucidation in ChIP-seq datasets with a knockout control. BioRxiv 10.1101/721720 [Preprint]. 2019. Available from:https://doi.org/10.1101/721720