RESUMO
Background: Genomic profiling efforts have revealed a rich diversity of oncogenic fusion genes. While there are many methods for identifying fusion genes from RNA-sequencing (RNA-seq) data, visualizing these transcripts and their supporting reads remains challenging. Findings: Clinker is a bioinformatics tool written in Python, R, and Bpipe that leverages the superTranscript method to visualize fusion genes. We demonstrate the use of Clinker to obtain interpretable visualizations of the RNA-seq data that lead to fusion calls. In addition, we use Clinker to explore multiple fusion transcripts with novel breakpoints within the P2RY8-CRLF2 fusion gene in B-cell acute lymphoblastic leukemia. Conclusions: Clinker is freely available software that allows visualization of fusion genes and the RNA-seq data used in their discovery.
Assuntos
Biologia Computacional/métodos , Proteínas de Fusão Oncogênica/genética , Análise de Sequência de RNA/métodos , Software , Processamento Alternativo , Mutação da Fase de Leitura , Perfilação da Expressão Gênica , Genômica , Humanos , Leucemia de Células B/genética , Leucemia-Linfoma Linfoblástico de Células Precursoras/genética , Linguagens de Programação , Domínios Proteicos , Isoformas de Proteínas , RNA/genética , Receptores de Citocinas/genética , Receptores Purinérgicos P2Y/genéticaRESUMO
Numerous methods have been developed to analyse RNA sequencing (RNA-seq) data, but most rely on the availability of a reference genome, making them unsuitable for non-model organisms. Here we present superTranscripts, a substitute for a reference genome, where each gene with multiple transcripts is represented by a single sequence. The Lace software is provided to construct superTranscripts from any set of transcripts, including de novo assemblies. We demonstrate how superTranscripts enable visualisation, variant detection and differential isoform detection in non-model organisms. We further use Lace to combine reference and assembled transcriptomes for chicken and recover hundreds of gaps in the reference genome.
