Bulk paired-end RNA-seq

Standard bulk RNA-seq on an Illumina sequencer: two paired-end cDNA reads, no cell barcode and no UMI. Every base is transcript sequence — there's nothing to demultiplex into cells. seqforge aligns these with plain STAR and counts genes, rather than STARsolo.

How it's read

• R1 and R2 are the two ends of the same cDNA fragment (a mate pair). Both are transcript sequence, typically 75–150 bp.
• No barcode, no UMI, no whitelist.

How seqforge tells it apart from single-cell

It's the absence of a barcode that identifies bulk. seqforge looks for a short, low-diversity technical read — the tell-tale of a cell barcode — and finds none, just two long, near-unique cDNA mates. A single-cell barcode read is short (26–28 bp) and repeats the same 16 bp prefix across reads; a bulk mate is long and near-unique from the first base, so a barcode read can never be mistaken for bulk cDNA.

Because this entry demands so little, it also serves as the fallback for any paired-end data. That's deliberate: when a real single-cell library (BD Rhapsody, SPLiT-seq) happens to share this loose shape, seqforge falls back to the barcode-list check to make sure it never quietly treats a single-cell library as bulk.

Coverage note

This is the paired-end, poly-A branch. Single-end bulk and explicit strand-protocol handling aren't modeled yet.

References

The exact, machine-readable definition seqforge uses lives in this entry's spec.yaml. (scg_lib_structs documents single-cell library structures; plain bulk RNA-seq isn't one of them, so there's no page to link.)