encode-toolkit

Search files across ALL experiments with combined experiment + file filters.

This is powerful for finding specific file types across many experiments.

Examples:

• All BED files from human pancreas ChIP-seq: file_format="bed", assay_title="Histone ChIP-seq", organ="pancreas"

• FASTQs from mouse liver RNA-seq: file_format="fastq", assay_title="RNA-seq", organ="liver", organism="Mus musculus"

• All IDR peak files for H3K27me3: output_type="IDR thresholded peaks", target="H3K27me3"

• BigWig signal tracks from ATAC-seq on brain tissue: file_format="bigWig", assay_title="ATAC-seq", organ="brain", biosample_type="tissue"

WHEN TO USE: Use to find specific file types across ALL experiments. More powerful than encode_list_files for cross-experiment file discovery. RELATED TOOLS: encode_list_files, encode_batch_download, encode_get_file_info

Args: file_format: File format ("fastq", "bam", "bed", "bigWig", etc.) file_type: Specific file type ("bed narrowPeak", "bed broadPeak", etc.) output_type: Output type ("reads", "peaks", "signal", etc.) output_category: Output category ("raw data", "alignment", "signal", "annotation") assembly: Genome assembly ("GRCh38", "hg19", "mm10") assay_title: Filter by assay type of parent experiment organism: Filter by organism of parent experiment organ: Filter by organ of parent experiment biosample_type: Filter by biosample type ("tissue", "cell line", etc.) target: Filter by ChIP/CUT&RUN target status: File status (default: "released") preferred_default: If True, only default/recommended files search_term: Free text search limit: Max results (default 25) offset: Skip first N results (pagination)

Returns: JSON with file results, total count, and pagination info.