Search Files Across Experiments
encode_search_filesSearch across all ENCODE experiments with combined experiment and file filters to locate specific file types like BED, FASTQ, or BigWig from particular assays, organs, or targets.
Instructions
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="total 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.
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| file_format | No | ||
| file_type | No | ||
| output_type | No | ||
| output_category | No | ||
| assembly | No | ||
| assay_title | No | ||
| organism | No | ||
| organ | No | ||
| biosample_type | No | ||
| target | No | ||
| status | No | released | |
| preferred_default | No | ||
| search_term | No | ||
| limit | No | ||
| offset | No |
Output Schema
| Name | Required | Description | Default |
|---|---|---|---|
| result | Yes |