10x Chromium Single Cell 3' Gene Expression v2¶
Droplet single-cell RNA-seq — the generation before v3. Every droplet holds one gel bead, which tags all of a cell's transcripts with the same cell barcode and each individual mRNA molecule with a unique UMI. That lets you count molecules per gene per cell.
How it's read¶
Two reads come off the sequencer:
| read | length | what it holds |
|---|---|---|
| R1 | 26 bp | a 16 bp cell barcode + a 10 bp UMI |
| R2 | open-ended | the cDNA (the transcript itself), read sense to the mRNA |
The cell barcode is drawn from 10x's published 737K-august-2016 list (~737,000 barcodes).
How seqforge tells v2 apart from v3¶
The only difference visible in the reads is R1 length: v2 is 16 + 10 = 26 bp; v3 is
16 + 12 = 28 bp. That 2 bp gap is decisive on its own, so seqforge separates v2 from v3 by
read geometry alone — before it ever consults a barcode list. The two are never confused. (Their
whitelists differ too — 737K-august-2016 vs 3M-february-2018 — but length settles it first.)
If a paper or database says "v2" while the reads are actually 28 bp, seqforge does not quietly pick one. It surfaces the disagreement (metadata says 26 bp, the bytes say 28 bp) and hands it to a human — the bytes decide what the data is.
Gotchas¶
- The barcode read can go missing on SRA.
fasterq-dumpwithout--include-technicaldrops R1 entirely; seqforge blocks rather than guessing which file is which. Re-fetch with--include-technical, or pull the submitter's original files. - SRA rewrites read-name headers, so seqforge never trusts them when grouping files into samples.
References¶
Read structure cross-checked against
scg_lib_structs — 10x Chromium 3'
(Teichmann Lab, CC-BY), which lays out the v2–v4 kits side by side. The exact, machine-readable
definition seqforge uses lives in this entry's spec.yaml.