Skill: Download GEO

Use When

• A user wants to download supplementary files (count matrices, CEL files, processed tables) for a GEO series (GSE) or sample (GSM).
• A user wants to download the series matrix file(s) for a GSE, which contain sample metadata and normalized expression values.
• A user wants to discover and fetch raw FASTQ files linked to a GEO series (which are stored in SRA and require download-sra).
• A user wants to bulk-download all supplementary files for a set of GSE accessions.
• A user wants to organize downloaded GEO files by sample or by file type.

Inputs

• Required:
  • one or more GEO accessions: GSE (series) or GSM (sample)
• Optional:
  • --type — what to download: supplementary (default), matrix, both, or sra-list
  • --outdir DIR — output directory (default: geo_downloads)
  • --filter PATTERN — glob pattern to select supplementary files (e.g., "*_counts.txt.gz", "*.CEL.gz")
  • --no-decompress — keep files compressed (default: leave as-is, do not auto-decompress)
  • --soft — also download the full SOFT metadata file for the series
  • --dry-run — list files that would be downloaded without fetching them

Workflow

1. Resolve the GEO FTP base path for the accession:
   • For GSEnnnnn where nnn is the numeric part:

     ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSEnnn/GSEnnnnn/

   • For GSEnnnnnnn (7-digit, prefix = GSEnnnnnn):

     ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSEnnnnnnn/GSEnnnnnnn/

   • Helper: PREFIX="${ACC%???}nnn" — replace last 3 digits with nnn.
2. List available files:

   curl -s "https://ftp.ncbi.nlm.nih.gov/geo/series/$PREFIX/$ACC/" 2>/dev/null
   # Or via NCBI GEO query API:
   curl -s "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=$ACC&targ=self&form=text&view=brief"

3. Download supplementary files (if --type supplementary or both):

   wget -r -nH --cut-dirs=5 -np -nd \
     -P "$OUTDIR/$ACC/supplementary/" \
     "https://ftp.ncbi.nlm.nih.gov/geo/series/$PREFIX/$ACC/suppl/"

   Apply --filter pattern if provided.
4. Download series matrix (if --type matrix or both):

   wget -r -nH --cut-dirs=5 -np -nd \
     -P "$OUTDIR/$ACC/matrix/" \
     "https://ftp.ncbi.nlm.nih.gov/geo/series/$PREFIX/$ACC/matrix/"

5. Download SOFT file (if --soft):

   wget -P "$OUTDIR/$ACC/soft/" \
     "https://ftp.ncbi.nlm.nih.gov/geo/series/$PREFIX/$ACC/soft/"

6. Extract SRA run accessions for raw FASTQ (if --type sra-list):

   esearch -db gds -query "$ACC[Accession]" | elink -target sra | \
     efetch -format runinfo | awk -F',' 'NR>1 && $1!="" {print $1}'

   Write the SRR list to $OUTDIR/$ACC/sra_accessions.txt and instruct the user to run download-sra with this file.
7. Report: files downloaded, total size, destination paths. For sra-list mode, display the SRR list and the recommended download-sra command.

Output Contract

• Supplementary files under <outdir>/<GSE>/supplementary/
• Series matrix files under <outdir>/<GSE>/matrix/ (plain text, gzip-compressed)
• SOFT file under <outdir>/<GSE>/soft/ (when --soft requested)
• sra_accessions.txt under <outdir>/<GSE>/ (when --type sra-list requested, one SRR per line)
• download_manifest.tsv listing: accession, file, size_bytes, url, local_path
• Recommended download-sra command when raw FASTQ is needed

Limits

• GEO FTP is accessible without authentication; no credentials are needed for public data.
• Supplementary files are whatever the submitter uploaded; format and content vary widely (CSV, TSV, CEL, H5AD, RDS, etc.).
• Series matrix files contain processed/normalized data, not raw counts. Raw counts, if available, are usually in supplementary files or in SRA.
• Raw sequencing data (FASTQ) is stored in SRA, not on the GEO FTP. Use download-sra with the sra_accessions.txt output of this skill to download raw reads.
• Some large GSE series have hundreds of supplementary files totalling many GB; always dry-run first to inspect file sizes.
• GEO does not provide MD5 checksums for supplementary files; integrity verification is not possible for supplementary downloads.
• Common failure cases:
  • FTP path resolution failure because the GSE numeric prefix is computed incorrectly; double-check the nnn suffix calculation
  • no supplementary files present (some series only have series matrix and SRA links)
  • wget following symlinks into unintended directories; use --no-parent flag
  • series matrix is split across multiple files (one per platform); all will be downloaded automatically