encode_batch_download
Search for ENCODE genomic data files matching specific criteria and download them in batch. Preview downloads first with dry-run mode, then execute to retrieve files like FASTQ, BAM, or BED formats based on organism, assay, or tissue parameters.
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="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", "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 |