Running multiplexed files

[mcortes-lopez]

Is it possible to implement sample demultiplexing (based on cell barcodes) within the pipeline? Currently I could only think about splitting the samples before running the pipeline(I can only think about Flexiplex as an option) or use genotypes to split afterwards, but then it would be good to have a way to only run part of the pipeline (before getting matrices of counts and expression)

[nrhorner]

Hi @mcortes-lopez.

This is not currently available with the workflow, but we will consider adding it in the future.
For now, you might be able to use this tool: https://github.com/10XGenomics/subset-bam