Question: When I run the "cellranger count" pipeline in Antibody-only mode (that is, without gene expression), the cloupe file is missing from the output folder. I hear that this is related to the number of Cell Surface Proteins (or antibodies/dextramers) used in the feature reference file. Could you add more color to this?
Answer: If there are less than 10 antibodies/dextramers in the feature reference file when analyzing the Cell Surface Protein library without an accompanying GEX library, Cell Ranger will skip the secondary analysis step. As a result, the analysis folder and the cloupe files are not output. Note that web summary metrics in the "Summary" tab and the feature barcode matrix are not impacted. Cell Surface Protein data, when run with accompanying GEX data, is also not affected regardless of the number of features in the feature reference.
Please note that working with less than 10 Cell Surface Proteins without an accompanying GEX library is officially not supported by 10x Genomics. However, for a workaround, if you are, you can pad the feature reference CSV file with additional lines of Cell Surface Proteins (that are not in your experiment). The padded Cell Surface Proteins will return zero UMI counts but enable Cell Ranger to run the complete pipeline, including generating the cloupe file.
Please also note that, in general, the choice of antibodies in the panel plays a significant role in the effectiveness of cell calling in Feature Barcoding only mode. See here for more details: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/no-gex-analysis.