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Fig. 1 | BMC Bioinformatics

Fig. 1

From: annoFuse: an R Package to annotate, prioritize, and interactively explore putative oncogenic RNA fusions

Fig. 1

Graphical representation of the annoFuse pipeline. RNA-seq data processed through STAR-RSEM and fusion calls generated by Arriba v1.1.0 and/or STAR-Fusion 1.5.0 are inputs for the pipeline. The fusion_standardization function standardizes calls from fusion callers to retain information regarding fused genes, breakpoints, reading frame information, as well as annotation from FusionAnnotator. Standardized fusion calls use fusion_filtering_QC to remove false positives such as fusions with low read support, annotated as read-throughs, found in normal and gene homolog databases and remove non-expressed fusions using expression_filter_fusion. Calls are annotated with annotate_fusion_calls to include useful biological features of interest (eg. Kinase, Tumor suppressor etc.) Project-specific filtering captures recurrent fused genes using functions to filter (shown in boxes) as well as putative driver fusion. Outputs available from annoFuse include TSV files of annotated and prioritized fusions, a PDF summary of fusions, recurrently-fused gene/fusion plots, and an HTML report. Finally, users can explore fusion data interactively using shinyFuse. (Created with BioRender.com)

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