Poster Presentation 40th Annual Lorne Genome Conference 2019

Measuring alternative polyadenylation from single cell RNA-seq with precision weights (#166)

Paul Harrison 1 , Sarah Williams 1 , David Albrecht 2 , David Powell 1 , Traude Beilharz 3
  1. Monash Bioinformatics Platform, Monash University, Clayton, VIC, Australia
  2. Faculty of Information Technology, Monash University, Clayton, VIC, Australia
  3. Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia

The 10x Genomics single cell RNA-seq method is 3' end focussed and can therefore be used to detect alternative polyadenylation (APA). We have developed a method for measuring APA, giving each gene a score between -1 and 1 representing a shift in 3' end site usage from the average. Measurement accuracy depends on the number of reads available, so precision weights (1/σ²) are also calculated for each measurement, similar to the voom method for gene expression data. Data in the form of a matrix of measurements with a matrix of precision weights can be used in a generic fashion for differential testing, exploratory factor analysis, or as part of a multi-omics analysis. The method is demonstrated on Peripheral Blood Mononuclear Cell data. APA is related cis-cell-trans-gene to expression levels, and top confidently APA genes are found.