Single-cell RNA-seq, LPS PBMC v3.1, Wave 2 STARsolo run (2026-05-08)
phalaena:run:PA-R-4-2-wave2-2026-05-08
Wave 2 run of paper 4.2 (resting vs LPS-4h human PBMC, 10x Chromium 3' v3.1, Erbon 2023). End-to-end through the cellseq pipeline (STARsolo against GRCh38, Scrublet, Scanpy) on both lanes, SUCCESS at 22:26Z on 2026-05-08 (followup #7). Run id bd8677bc.... Recovered 5,915 cells on the resting (ctrl) lane and 6,789 cells on the LPS-4h (stim) lane, both at 100 percent valid barcodes, roughly 33,000 genes detected. This run empirically validates --soloBarcodeReadLength 0 (validation finding #22): Erbon's R1 is 29 nt against the expected 28 nt (16 CB + 12 UMI), and STAR's barcode-length check rejects the read without the flag.
- kind
- run
- pipeline
- Single-cell RNA-seq pipeline, release p1.1
- status
- reviewed
- googlebatch:bd8677bc...
- phalaena:run:bd8677bc
View Single-cell RNA-seq, LPS PBMC v3.1, Wave 2 STARsolo run (2026-05-08) on the Phalaena Wiki