I'm using CellRanger to analyze some RNA-seq data I have but I'm having a bit of trouble knowing if I'm doing the preprocessing steps correctly. This is the folder of Fastqs that I have:

Control_GEX_S1_L003_I1_001.fastq.gz    Treatment_BCR_S6_L004_R2_001.fastq.gz
Control_GEX_S1_L003_I2_001.fastq.gz    Treatment_GEX_S2_L003_I1_001.fastq.gz
Control_GEX_S1_L003_R1_001.fastq.gz    Treatment_GEX_S2_L003_I2_001.fastq.gz
Control_GEX_S1_L003_R2_001.fastq.gz    Treatment_GEX_S2_L003_R1_001.fastq.gz
Control_GEX_S1_L004_I1_001.fastq.gz    Treatment_GEX_S2_L003_R2_001.fastq.gz
Control_GEX_S1_L004_I2_001.fastq.gz    Treatment_GEX_S2_L004_I1_001.fastq.gz
Control_GEX_S1_L004_R1_001.fastq.gz    Treatment_GEX_S2_L004_I2_001.fastq.gz
Control_GEX_S1_L004_R2_001.fastq.gz    Treatment_GEX_S2_L004_R1_001.fastq.gz
FASTQ Files-selected (3).zip           Treatment_GEX_S2_L004_R2_001.fastq.gz
FASTQ Files-selected (4).zip           Treatment_TCR_S4_L003_I1_001.fastq.gz
FASTQ Files-selected.zip               Treatment_TCR_S4_L003_I2_001.fastq.gz
Matrix Files (1).zip                   Treatment_TCR_S4_L003_R1_001.fastq.gz
Treatment_BCR_S6_L003_I2_001.fastq.gz  Treatment_TCR_S4_L003_R2_001.fastq.gz
Treatment_BCR_S6_L003_R1_001.fastq.gz  Treatment_TCR_S4_L004_I1_001.fastq.gz
Treatment_BCR_S6_L003_R2_001.fastq.gz  Treatment_TCR_S4_L004_I2_001.fastq.gz
Treatment_BCR_S6_L004_I1_001.fastq.gz  Treatment_TCR_S4_L004_R1_001.fastq.gz
Treatment_BCR_S6_L004_I2_001.fastq.gz  Treatment_TCR_S4_L004_R2_001.fastq.gz
Treatment_BCR_S6_L004_R1_001.fastq.gz

As I understand it, there are four samples here: "Control_GEX," "Treatment_GEX," "Treatment_TCR," and "Treatment_BCR" (although I wasn't sure if there may be at least 6 samples overall because I see that there are "S1," "S2," "S4," "S6" after the sample names). I've been running "cellranger count" on each sample. Is this generally correct? It runs successfully for the first three samples but it generates this error for "Treatment_BCR":

[error] Pipestance failed. Error log at:
Treatment_BCR/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_CHEMISTRY_DETECTOR/_GEM_WELL_CHEMISTRY_DETECTOR/DETECT_COUNT_CHEMISTRY/fork0/chnk0-ufe99c8e697/_errors

Log message:
Unable to distinguish between [SC5P-R2, SC3Pv2] chemistries based on the R2 read mapping for Sample Treatment_BCR in "/projects/p32525/RNAseq_data/Fastqs".
Total Reads          = 100000
Mapped reads         = 72021
Sense reads          = 13294
Antisense reads      = 26340

In order to distinguish between the 3' vs 5' assay configuration the following conditions need to be satisfied:
- A minimum of 1000 confidently mapped reads
- A minimum of 5.0% of the total reads considered needs to be confidently mapped
- The number of sense reads need to be at least 2x compared to the antisense reads or vice versa

Please validate the inputs and/or specify the chemistry via the --chemistry argument.


Waiting 6 seconds for UI to do final refresh.
Pipestance failed. Use --noexit option to keep UI running after failure.

2021-12-26 16:03:47 Shutting down.

I'm not quite sure how to resolve this - "cellranger count" worked for all the other samples, and I'm not quite sure what "--chemistry" argument I would specify here. I'm working with data someone else generated and I don't have access to the experimental set up - would I find or be able to infer that "--chemistry" argument?

EDIT:

Also, I haven't been able to find a clear explanation of what "GEX" means, and why "BCR," "TCR," and "GEX" are used - is this multiplexing? Also I'm not quite sure in a very basic way how "BCR," "TCR," and "GEX" are used