The BUS Format for Single-Cell RNA-Seq Processing and Analysis

The Barcode-UMI-Set format (BUS) is a recently developed format for representing pseudoalignments of reads from single-cell RNA-seq experiments. The format can be used with most single-cell RNA-seq technologies, can be generated efficiently, and allows for development of modular and robust workflows for processing and analysis of single-cell RNA-seq reads. To demonstrate the utility of BUS, we processed 381,992,071 single-cell RNA-Seq reads from a 1:1 mixture of fresh frozen human cells (HEK293T) and mouse cells (NIH3T3) produced with 10x technology and hosted on the 10x Genomics website. The generation of BUS format using a new command in the kallisto program took 984 seconds for this data (in comparison with 55,745 seconds with the 10x Genomics CellRanger software). I will present results showing that this workflow not only produces comparable results to the existing standard workflow, but is flexible and useful for many other applications. Presenter: Fan Gao. This is joint work with Eduardo da Veiga Beltrame, Jase A. Gehring, Kristj¡n E. Edljarn Hjoerleifsson, Lambda Lu, Paull Melsted, Vasilis Ntranos, Lior Pachter, and Valentine Svensson.