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Module 8 — Pull One Single-Cell FASTQ (Public SRA/ENA)

Time: 60–90 min
Goal: Find a study, choose one small run, download the FASTQ via HTTPS, and verify it.

What you'll practice

  • Navigating SRA (Study → Sample → Experiment → Run (SRR))
  • Using the Run Selector to find a small run
  • Grabbing direct ENA HTTPS links for FASTQ
  • Resumable downloads and checksums

1) Pick a study

Use a classic human single-cell embryo dataset such as SRP011546 (GEO GSE36552).
Open the Run Selector for the study. Sort by size/spots and pick a small SRR.

Tip

If your choice is still large, that's okay—download just one file and downsample in the next module.

2) Get the direct FASTQ URL

From the SRR page, follow the ENA / EBI link. On the ENA run page, copy an HTTPS FASTQ link (R1 or single-end).

3) Download (resumable) and verify

mkdir -p ~/de-onramp/lesson5/data && cd ~/de-onramp/lesson5/data

# Replace with your URL:
wget -c "https://.../SRRxxxxxxx.fastq.gz" -O SRR.fastq.gz

# Optional: if ENA provides checksums, verify; otherwise compute your own
sha256sum SRR.fastq.gz > SRR.fastq.gz.sha256
sha256sum -c SRR.fastq.gz.sha256

# Sanity peek (don't expand the whole file!):
zcat SRR.fastq.gz | head -n 8

mkdir -p ~/de-onramp/lesson5/data && cd ~/de-onramp/lesson5/data

# Replace with your URL:
wget -c "https://.../SRRxxxxxxx.fastq.gz" -O SRR.fastq.gz

# Optional: if ENA provides checksums, verify; otherwise compute your own
shasum -a 256 SRR.fastq.gz > SRR.fastq.gz.sha256
shasum -a 256 -c SRR.fastq.gz.sha256

# Sanity peek (don't expand the whole file!):
gzcat SRR.fastq.gz | head -n 8

If the file is very large and head feels slow, use pv or zcat/gzcat | head as above (fast). If you need to stop, Ctrl-C and rerun wget -c later to resume.

4) (Optional) Keep a tiny working copy

conda activate rnaseq101
seqtk sample -s 7 SRR.fastq.gz 10000 | gzip > SRR.10k.fastq.gz   # ~10k reads

Exit Ticket (email)

Subject: DE M8 Exit Ticket –
Paste:

  • The study accession and the SRR you chose
  • Your exact wget command (with URL redacted if you prefer)
  • File size (ls -lh) and the single line from checksum verification (sha256sum -c or shasum -a 256 -c)