After discussion about the benchmarking analysis, we decided to default to using the pre-mRNA index as the default index with all single nuclei RNA seq samples for alevin-fry and use the --include-introns flag when running cellranger.
The workflows for alevin-fry and cellranger should be updated accordingly so we no longer need to separate sample runs by cell or nucleus or have a parameter option at the command line.
After discussion about the benchmarking analysis, we decided to default to using the pre-mRNA index as the default index with all single nuclei RNA seq samples for alevin-fry and use the
--include-intronsflag when running cellranger.The workflows for alevin-fry and cellranger should be updated accordingly so we no longer need to separate sample runs by cell or nucleus or have a parameter option at the command line.