OmniPeak

OmniPeak is a universal HMM-based peak caller capable of processing a broad range of ChIP-seq, ATAC-seq, and single-cell ATAC-seq datasets of different quality.

Features

• Supports both narrow and broad footprint experiments (ChIP-seq, ATAC-seq, DNAse-seq)
• Supports BAM, SAM, CRAM, BED, BigWig input formats
• Produces robust results on datasets of different signal-to-noise ratio, including Ultra-Low-Input ChIP-seq
• Produces highly consistent results in multiple-replicates experiment setup
• Tolerates missing control experiment
• Integrated into the JetBrains Research ChIP-seq analysis pipeline from raw reads to visualization and peak calling
• Integrated with the JBR Genome Browser, uploaded data model allows for interactive visualization and fine-tuning
• Experimentally supports multi-replicated mode and differential peak calling mode

Requirements

Download and install Java 21+.

Peak calling

To analyze a single (possibly replicated) biological condition use analyze command. See details with command:

$ java --add-modules=jdk.incubator.vector  -Xmx8G  -jar omnipeak.jar analyze --help

The <output.bed> file will contain predicted and FDR-controlled peaks in the ENCODE broadPeak (BED 6+3) format:

<chromosome> <peak start offset> <peak end offset> <peak_name> <score> . <coverage or fold/change> <-log p-value> <-log Q-value>

Examples on Java 21:

• Regular peak calling
  java --add-modules=jdk.incubator.vector -Xmx8G -jar omnipeak.jar analyze -t ChIP.bam -c Control.bam --cs Chrom.sizes -p Results.peak
• Model fitting only
  java --add-modules=jdk.incubator.vector -Xmx8G -jar omnipeak.jar analyze -t ChIP.bam -c Control.bam --cs Chrom.sizes -m Model.op

Differential peak calling

Experimental! To compare two (possibly replicated) biological conditions use the compare. See help for details:

$ java --add-modules=jdk.incubator.vector -Xmx8G -jar omnipeak.jar compare --help

Command line options

Parameter	Description
-t, --treatment TREATMENT required	Treatment file. Supported formats: BAM, BED, or BED.gz file. If multiple files are provided, they are treated as replicates. Multiple files should be separated by commas: -t A,B,C. Multiple files are processed as replicates on the model level.
-c, --control CONTROL	Control file. Multiple files should be separated by commas. A single control file, or a separate file per each treatment file is required. Follow the instructions for -t, --treatment.
-cs, --chrom.sizes CHR_SIZES required	Chromosome sizes file for the genome build used in TREATMENT and CONTROL files. Can be downloaded at UCSC.
-b, --bin BIN_SIZE	Peak analysis is performed on read coverage tiled into consequent bins of configurable size.
-f, --fdr FDR	False Discovery Rate cutoff to call significant regions.
-p, --peaks PEAKS	Resulting peaks file in ENCODE broadPeak* (BED 6+3) format. If omitted, only the model fitting step is performed.
-chr, --chromosomes CHROMOSOMES	Chromosomes to process, multiple chromosomes should be separated by commas.
-fmt, --format FORMAT	Reads file format. Supported: BAM, SAM, CRAM, BED. Text format can be in zip or gzip archive. If not provided, guessed from file extensions.
-fr, --fragment FRAGMENT	Fragment size. If provided, reads are shifted appropriately. If not provided, the shift is estimated from the data. --fragment 0 is recommended for ATAC-Seq data processing.
-kd, --keep-duplicates	Keep duplicates. By default, OmniPeak filters out redundant reads aligned at the same genomic position. Recommended for bulk single cell ATAC-Seq data processing.
-bl, --blacklist BLACKLIST_BED	Blacklisted regions of the genome to be excluded from peak calling results.
-m, --model MODEL	This option is used to specify OmniPeak model path.
-w, --workdir PATH	Path to the working directory. Used to save coverage and model cache.
-sm, --summits	Calls summits within peaks. Recommended for ATAC-seq and single-cell ATAC-seq analysis.
-l, --log LOG	Path to log file, if not provided, it will be created in working directory.
-d, --debug	Print debug information, useful for troubleshooting.
-q, --quiet	Turn off standard output.
-thr, --threads THREADS	Configure the parallelism level.
-bw, --bigwig BIGWIG_PATH	Create beta-control corrected counts per million normalized track.
--iterations ITS	Maximum number of iterations for Expectation Maximisation (EM) algorithm.
--threshold THR	Convergence threshold for EM algorithm, use --debug option to see detailed info.
--hmm-snr SNR	Fraction of coverage to estimate and guard signal to noise ratio, 0 to disable constraint check.
--hmm-low LOW	Minimal low state mean threshold, guards against too broad peaks, 0 to disable constraint check.
--sensitivity SENSITIVITY	Configures log PEP threshold sensitivity for candidates selection. Automatically estimated from the data, or during semi-supervised peak calling.
--gap GAP	Configures minimal gap between peaks. Generally, not required, but used in semi-supervised peak calling.
--multiple TEST	Method applied for multiple hypothesis testing. BH for Benjamini-Hochberg, BF for Bonferroni.
--fragmentation FRAGMENTATION	Fragmentation threshold in bp to apply compensation gap. Fragmentation indicates how much less peaks we could obtain by increasing gap. Not available when gap is explicitly provided.
--clip CLIP_TRESHOLD	Clip max threshold for fine-tune boundaries according to local signal, 0 to disable.
--ext	Save extended states information to model file. Required for model visualization in JBR Genome Browser.
--deep-analysis	Deep analysis of model including analysis of coverage / candidates / peaks.
--keep-cache	Keep cache files. By default OmniPeak creates cache files in working directory and cleans up.

Build from sources

Clone bioinf-commons library under the project root.

git clone [email protected]:JetBrains-Research/bioinf-commons.git

Launch the following command line to build OmniPeak jar:

./gradlew shadowJar

The OmniPeak jar file will be generated in the folder build/libs.

Errors Reporting

Use GitHub issues to suggest new features or report bugs.

Authors

JetBrains Research BioLabs