How to use Salmon/Alevin to preprocess CITE-seq data

Introduction

A state-of-the-art method called CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by Sequencing) allows surface protein levels and RNA expression to be measured simultaneously in individual cells. CITE-seq uses traditional single-cell RNA-sequencing to read out both transcriptome and proteomic information from the same cell after labeling it with oligo-conjugated antibodies. This gets over the …