Cortexa research tool·genomics·encode

ENCODE List Files

List ENCODE data files with filters by file format, output type, or assay. Returns file metadata including accessions, formats (FASTQ, BAM, bigWig), output types (alignments, peaks, signal), and file sizes. Use this to programmatically discover downloadable artifacts for specific experiments or data types. Find file accessions to use with ENCODE_get_file for detailed file information and download URLs.

Livelast probed 2026-05-01 01:00Z· 2896msCortexa

Status

The most recent probe succeeded. Safe to call from the agent today.

Last probed: 1d ago
Last success: 1d ago
Last latency: 2896ms

Schema

JSON Schema the agent (or your API call) must match.

{
  "properties": {
    "assay_title": {
      "description": "Assay filter (e.g., 'ChIP-seq', 'RNA-seq'). Filters files by the experimental assay that generated them.",
      "type": "string"
    },
    "file_type": {
      "description": "File format filter (e.g., 'fastq', 'bam', 'bigWig', 'bed'). Common formats: fastq (raw reads), bam (alignments), bigWig (coverage), bed (peaks/regions).",
      "type": "string"
    },
    "limit": {
      "default": 10,
      "description": "Maximum number of results to return (1–100).",
      "maximum": 100,
      "minimum": 1,
      "type": "integer"
    }
  },
  "type": "object"
}

Examples (1)

Default ENCODE List Files call

public-safeinput

{
  "limit": 3
}

Expected response keys: success

Anonymous-safe example. Rate-limited; no sign-in required.

Identifiers

Catalog ID: tu_ENCODE_list_files
Tool name: ENCODE_list_files
Added: 2026-05-01 00:58Z
Tags: tooluniverse

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