Bulk Illumina RNA-seq

Standard bulk RNA-seq on an Illumina sequencer: cDNA reads with 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.

Paired-end and single-end are one entry, not two. They are the same chemistry run two ways, so this entry declares the paired layout and names R1 alone as its single-end configuration; the bytes choose between them, and a deposit of one file is explained rather than refused. Nothing about the reads is written down twice, so the two configurations cannot drift apart.

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 poly-A branch. Explicit strand-protocol handling isn'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.)