CellRanger 2.6.1 with multixplex FRP

[anavia93]

I'm following the "read the docks" input protocol for the CSV file and other Terra inputs and am receiving an error related to the chemistry input. The default chemistry seems to omit the mfrp chemistry and as such, I'm getting a "An extremely low rate of correct barcodes was observed for all the candidate chemistry choices for the input" message and "pipestance failed" message. I've tried adding the frp chemistry whitelist file from 10X's "737k-fixed-rna-profiling.txt" under the acronym_file input, but it is flagged as being too large of a file. This file is just a list of barcodes, which may not match the intended file format. Is there a specific input I can call to ensure frp chemistry is reference? Thanks!

[yihming]

Hi @anavia93 ,

I was able to use the cellranger workflow to successfully apply to the case of "Multiplex FRP, multiple Probe Barcodes/sample". In the input sample sheet, since there is no "Chemistry" column, then cellranger will assign "auto" for the sample which is cellranger's recommended way.

May I know which FRP setting that your data belong? You may refer to the examples in https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/multi-frp#examples.

If you don't trust "auto" which cellranger would automatically determines the chemistry, you may explicitly specify "Chemistry" column by choosing keywords from https://www.10xgenomics.com/support/software/cell-ranger/latest/advanced/cr-multi-config-csv-opts#chem-opts.

The chemistry whitelist entries in the acronym_file is for the feature barcoding step. In the context of FRP, if your data contain antibody modality, then this can be critical. Otherwise, if your data only contain the GEX modality, you don't need to worry about it.