Fig. 1
From: Sierra: discovery of differential transcript usage from polyA-captured single-cell RNA-seq data
Sierra workflow. Sierra starts with a BAM file produced by an alignment program such as CellRanger. Standard gene-level workflow (top row) involves using a gene model to produce a matrix of gene-level counts used for clustering. The Sierra pipeline performs splice-aware peak calling to identify coordinates corresponding to potential polyadenylation sites. Peak coordinates are used to build an annotated UMI count matrix for each gene peak. This new data can be used to identify genes showing differential peak usage, with visualisation options for plotting relative peak expression and read coverage across selected cell populations