Swimming downstream: statistical analysis of differential transcript usage following Salmon quantification

Michael I. Love, Charlotte Soneson, Rob Patro
2018 F1000Research  
Detection of differential transcript usage (DTU) from RNA-seq data is an important bioinformatic analysis that complements differential gene expression analysis. Here we present a simple workflow using a set of existing R/Bioconductor packages for analysis of DTU. We show how these packages can be used downstream of RNA-seq quantification using the Salmon software package. The entire pipeline is fast, benefiting from inference steps by Salmon to quantify expression at the transcript level. The
more » ... orkflow includes live, runnable code chunks for analysis using DRIMSeq and DEXSeq, as well as for performing two-stage testing of DTU using the stageR package, a statistical framework to screen at the gene level and then confirm which transcripts within the significant genes show evidence of DTU. We evaluate these packages and other related packages on a simulated dataset with parameters estimated from real data.
doi:10.12688/f1000research.15398.3 fatcat:ef3cg4vrorfhzkl3o5bgiduahi