Step 0: Acquire Data (GEO/SRA Only)
Step 0: Acquire Data (GEO/SRA Only)
Skip this step if user has local FASTQ files.
For public datasets, fetch from GEO/SRA first. See references/geo-sra-acquisition.md for the full workflow.
Quick start:
# 1. Get study info
python scripts/sra_geo_fetch.py info GSE110004
# 2. Download (interactive mode)
python scripts/sra_geo_fetch.py download GSE110004 -o ./fastq -i
# 3. Generate samplesheet
python scripts/sra_geo_fetch.py samplesheet GSE110004 --fastq-dir ./fastq -o samplesheet.csv
DECISION POINT: After fetching study info, confirm with user:
- Which sample subset to download (if multiple data types)
- Suggested genome and pipeline
Then continue to Step 1.