Macs3 Tools

Configuration File: remote_tools/macs3_tools.json Tool Type: Remote Tools Count: 1

This page contains all tools defined in the macs3_tools.json configuration file.

Available Tools

run_macs3_callpeak (Type: RemoteTool)

Call ChIP-seq / ATAC-seq peaks from an aligned reads file with MACS3 callpeak (Model-based Anal…

run_macs3_callpeak tool specification

Tool Information:

  • Name: run_macs3_callpeak

  • Type: RemoteTool

  • Description: Call ChIP-seq / ATAC-seq peaks from an aligned reads file with MACS3 callpeak (Model-based Analysis of ChIP-Seq; Zhang et al., Genome Biology 2008; macs3-project successor). Models read enrichment over a background/input control to identify regions of significant signal — the field-standard first analysis step after alignment. Input is a server-accessible BAM/BED/BED-PE alignment file; returns the number of peaks, the top-N peaks by score, and summary statistics, parsed from the ENCODE narrowPeak output.

Parameters:

  • treatment (string) (required) Server-accessible path to the treatment/ChIP alignment file (BAM/BED/BED-PE).

  • control (string) (optional) Server-accessible path to the input/control alignment file (optional but recommended).

  • format (string) (optional) Input format: AUTO (default), BAM, BED, BAMPE, or BEDPE. Use BAMPE/BEDPE for paired-end (e.g. ATAC-seq).

  • genome_size (string) (optional) Effective genome size: ‘hs’ (human, default), ‘mm’ (mouse), ‘ce’ (worm), ‘dm’ (fly), or a number (e.g. ‘2.7e9’).

  • qvalue (number) (optional) q-value (minimum FDR) cutoff to call significant peaks (default 0.05).

  • top_n (integer) (optional) Number of top peaks (by score) to return (default 50).

  • nomodel ([‘boolean’, ‘null’]) (optional) Skip the shift-model step (pass –nomodel –extsize). Required for ATAC-seq / single-end data where model building fails. Default false.

  • extsize ([‘integer’, ‘null’]) (optional) Fragment extension size used with nomodel (default 200; ~147 for ATAC).

Example Usage:

query = {
    "name": "run_macs3_callpeak",
    "arguments": {
        "treatment": "example_value"
    }
}
result = tu.run(query)