We received 10x single cell Flex data from a collaborator, it appears to have been run with

$ /cellranger/cellranger-7.1.0/cellranger multi \
    --id=${sample_id} \
    --csv=/${sample_id}.csv

$ cat ${sample_id}.csv
[gene-expression]
reference,/10xgenomics/refdata-gex-GRCh38-2020-A
probe-set,/cellranger/cellranger-7.1.0/probe_sets/Chromium_Human_Transcriptome_Probe_Set_v1.0.1_GRCh38-2020-A.csv

[libraries]
fastq_id,fastqs,feature_types
${sample_id},/FASTQS/outs/fastq_path/${sample_id}/,Gene Expression

I am trying to map these to nf-core/scrnaseq parameters

--aligner cellrangermulti \
--cellranger_vdj_index /10xgenomics/refdata-gex-GRCh38-2020-A \
--gex_frna_probe_set /cellranger/cellranger-7.1.0/probe_sets/Chromium_Human_Transcriptome_Probe_Set_v1.0.1_GRCh38-2020-A.csv \
...

I am not sure what VDJ means though. If

--cellranger_index

is also used for cellrangermulti, is that more appropriate? Is there anything else I am missing?

Hi there, Depending on your analysis, both indexes will be used. The normal cellranger index is the normal reference for the expression analysis and the vdj is the reference for the antibody analysis.