encode-toolkit

List all files for a specific ENCODE experiment, with optional filters.

Examples:

• All BED files: experiment_accession="ENCSR133RZO", file_format="bed"

• FASTQs only: experiment_accession="ENCSR133RZO", file_format="fastq"

• Signal tracks: experiment_accession="ENCSR133RZO", output_category="signal"

• Default/recommended files: preferred_default=True

• Peaks from GRCh38: file_format="bed", output_type="IDR thresholded peaks", assembly="GRCh38"

Common file_format values: "fastq", "bam", "bed", "bigWig", "bigBed", "tsv", "hic"

Common output_type values: "reads", "alignments", "signal of unique reads", "signal of all reads", "fold change over control", "IDR thresholded peaks", "pseudoreplicated peaks", "replicated peaks", "gene quantifications", "transcript quantifications", "contact matrix"

WHEN TO USE: Use to browse files within a known experiment. Use encode_search_files instead to find files across experiments. RELATED TOOLS: encode_search_files, encode_get_file_info, encode_download_files

Args: experiment_accession: ENCODE experiment accession (e.g., "ENCSR133RZO") file_format: Filter by format ("fastq", "bam", "bed", "bigWig", "bigBed", etc.) file_type: Filter by specific type ("bed narrowPeak", "bed broadPeak", etc.) output_type: Filter by output type ("reads", "peaks", "signal", etc.) output_category: Filter by category ("raw data", "alignment", "signal", "annotation") assembly: Filter by genome assembly ("GRCh38", "hg19", "mm10") status: Filter by status ("released", "archived", "in progress") preferred_default: If True, return only default/recommended files limit: Max files to return (default 200)

Returns: JSON list of files with accession, format, size, download URL, and metadata.