Commands for processing mixed 4-sample scRNA-seq data with cellranger

Question

[Apprentice]

We processed and mixed four samples with Chromium's library kit to perform scRNA-seq. As result we obtained on a set of fastq files (I1, I2, R1, R2).We would like to do the mapping and quantification per gene on a per sample basis. In this case, the cellranger count command cannot be used. How can we perform the process we want with cellranger? Please let us know.

[ATpoint]

How did you achieve the sample separation in the lab? Hashtag oligos?

[Apprentice]

Thank you for your comment. After hybridizing the detection probes of the Chromium Fixed RNA Kit to the RNA sample obtained from each of the four subjects, I performed a ligation reaction to combine the probes that had hybridized next to each other. After mixing four RNA samples so that the cell count was equal, ChromiumX was used to encapsulate the cells with barcode-labeled primer beads, and the probes and primers were annealed and elongated to add the cell-identification adapter sequence to the detection probes.

[ATpoint]

I am not 100% familiar with the library protocol. Do the probes per sample have a unique barcode or not?

[Apprentice]

Thank you for your further comments. A unique barcode is assigned to each sample.