CICERO

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CICERO (Clipped-reads Extended for RNA Optimization) is an assembly-based algorithm to detect diverse classes of driver gene fusions from RNA-seq.

CICERO is maintained on GitHub at https://github.com/stjude/Cicero. The source code is freely available for academic use. Please check the manual on GitHub.

Demo

1 MV4_11 cell line has FLT3 internal tandem duplication (ITD) (PMID: 12529668)
The raw RNA-seq data are downloaded from SRR6049668, and the bam file is from STAR mapping.

• MV4_11_RNAseq_1.bam
• MV4_11_RNAseq_1.bam.bai
• CICERO v1.7.0 GRCh37-lite output: MV4_11_final_fusions.txt

2 Nalm6 cell line has IGH-DUX4 fusion (PMID:27776115)
The bam file is from PMID:27776115

• SJBALL020016_C27.bam
• SJBALL020016_C27.bam.bai
• CICERO v1.7.0 GRCh37-lite output: SJBALL020016_C27_final_fusions.txt