Model-based analysis of sample index hopping reveals its widespread artifacts in multiplexed single-cell RNA-sequencing

Supplementary data that are needed to rerun the reproducible notebooks from the first steps using Alevin output and configuration files.

Intermediate R data object that can be used to rerun the reproducible notebooks after the filtering steps.

Validation data for inferring the sample index hopping rate. The hiseq4000_joined_datatable_plexed_nonplexed.zip file contains read counts for four samples (two non-multiplexed and two multiplexed)  joined by  a cell-barcode, UMI, and gene-ID (CUG) key combination. The hiseq4000_inner_joined_with_labels.zip file contains only those CUGs that are observed in both the non-multiplexed and multiplexed samples.