I submitted in house lab-made libraries to a core to run our scRNA-seq. The libraries were made using a 5’ V2 PE kit. Dual index. So we got I1, I2, R1 and R2 GEX FASTQs back for each sample (we also made TCR libraries with a V1.1 kit). When I run these 4 files through CellRanger and let the chemistry get auto-detected, the summary HTML file tells me the chemistry is ‘Single Cell 5’ R2-only’. I tried to run it through Cellranger setting the chemistry argument to 5’ PE, but the summary file said no cells were detected. It reports no reads were found in the R1 file. I looked at the R1 FASTAs and they don’t look odd. They show a short barcode sequence + UMI.

I’m worried that if Cellranger is actually only processing the R2 reads, I am not getting accurate data. Why are the R1 reads not being processed?Has anyone had experience with this?