Calculating Relative Chimeric RNA Expression with FusionBlaster

Chimeric RNA molecules-formed from nucleotide sequences of multiple genes-can arise through chromosomal rearrangements, transcriptional read-through events, or trans-splicing between distinct transcripts. These chimeric RNAs have been shown to play functional roles in both disease states and normal physiological processes, underscoring their biological relevance. Despite this, there are currently a limited number of tools available that aim to quantify chimeric RNA expression. Here, we introduce a metric called the Relative Index of Chimeric Expression (RICE), which assesses the expression of chimeric transcripts relative to their corresponding wild-type parental transcript, and we describe an easy-to-use bioinformatic tool called FusionBlaster for calculating RICE values from RNA sequencing data. After following this guide, users can apply the FusionBlaster pipeline to perform differential RICE analysis on their own RNA sequencing data by applying the appropriate statistical methods.