Batch Search and Download
encode_batch_downloadSearch for ENCODE files by criteria like format, assay, or organism, then preview or download all matching files in batch.
Instructions
Search for files and download them all in batch.
First searches for files matching the criteria, then downloads them. By default runs in dry_run mode to preview what would be downloaded. Set dry_run=False to actually download.
WHEN TO USE: Use for searching and downloading files in one step. Always use dry_run=True first to preview. For specific file accessions, use encode_download_files. RELATED TOOLS: encode_download_files, encode_search_files
Examples:
Download all BED files from human pancreas ChIP-seq: file_format="bed", assay_title="Histone ChIP-seq", organ="pancreas", download_dir="/data/encode", dry_run=False
Preview FASTQ downloads for mouse brain RNA-seq: file_format="fastq", assay_title="total RNA-seq", organ="brain", organism="Mus musculus", download_dir="/data/encode"
Download IDR peaks for H3K27me3 in GRCh38: output_type="IDR thresholded peaks", target="H3K27me3", assembly="GRCh38", download_dir="/data/encode", dry_run=False
Args: download_dir: Local directory to save files file_format: File format filter ("fastq", "bam", "bed", "bigWig", etc.) output_type: Output type filter ("reads", "peaks", "signal", etc.) output_category: Output category ("raw data", "alignment", "annotation", etc.) assembly: Genome assembly ("GRCh38", "mm10", etc.) assay_title: Assay type ("Histone ChIP-seq", "ATAC-seq", "total RNA-seq", etc.) organism: Organism (default: "Homo sapiens") organ: Organ/tissue ("pancreas", "brain", "liver", etc.) biosample_type: Biosample type ("tissue", "cell line", "primary cell", etc.) target: ChIP/CUT&RUN target ("H3K27me3", "CTCF", etc.) preferred_default: If True, only download default/recommended files organize_by: File organization ("flat", "experiment", "format", "experiment_format") verify_md5: Verify downloads with MD5 checksums (default True) limit: Max files to download (default 100, safety limit) dry_run: If True (default), only preview what would be downloaded. Set False to download.
Returns: JSON with download preview (dry_run=True) or download results (dry_run=False).
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| download_dir | Yes | ||
| file_format | No | ||
| output_type | No | ||
| output_category | No | ||
| assembly | No | ||
| assay_title | No | ||
| organism | No | Homo sapiens | |
| organ | No | ||
| biosample_type | No | ||
| target | No | ||
| preferred_default | No | ||
| organize_by | No | experiment | |
| verify_md5 | No | ||
| limit | No | ||
| dry_run | No |
Output Schema
| Name | Required | Description | Default |
|---|---|---|---|
| result | Yes |