10x genomics – Running cellranger on scRNASeq data with feature barcoding (10x + antibody capture)

I can’t seem to find a clear answer to this question, so here it goes:

I have sequenced scRNASeq + scVDJSeq (TCR) data, which has been sequenced using feature barcoding from 10x genomics, via antibody capture.

There is a very useful cellranger multi command, which allows us to process both this data types in ‘one go’.

In order to run it one needs to generate a csv file a priori, such that cellranger is able to identify which files are pertinent to which file type – see this link:support.10xgenomics.com/single-cell-vdj/software/pipelines/latest/using/multi

In the link above, with the example given under “Example multi config CSVs”, it seems as though there are separate fastq files for the feature barcode, versus for the actual gene expression samples. Whereas, in my case, I only have the standard R1 and R2 fastq files, which is creating some confusion as how to generate this file, and run cellranger.

Now my question is, how does one run cellranger multi with feature barcoding should there only be the standard 2 fastq files? My understanding is that the feature barcode is usually in the R2 read? Is this correct? Would I need to Demultiplex? I am completely lost as to how to proceed. If you know, could you please provide a short example of what your csv files would look like, should you not have separate fastq files for the feature barcode files?


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