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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.
- 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
Download and install Java 21+.
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 --helpThe <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
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| Parameter | Description |
|---|---|
-t, --treatment TREATMENTrequired | 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_SIZESrequired | 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. |
-ncr, --no-control-regression | Don't regress control track data from the treatment data. |
-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.Disabled when processing BigWig files. |
--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. |
Clone bioinf-commons library under the project root.
git clone git@github.com: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.
Use GitHub issues to suggest new features or report bugs.