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Clinker is a bioinformatics pipeline that generates a superTranscriptome from popular fusion finder outputs (JAFFA, tophatFusion, SOAP, deFUSE, etc), that can be then be either viewed in genome viewers such as IGV or through the included plotting feature.
Inter-chromosomal translocation can result in a fusion between two genes, which in turn, can be oncogenic or have tumour suppressing regions excised. Such fusions are therefore indicative of cancers such as chronic myelogenous leukemia (CML), acute lymphoblastic leukemia (ALL) and acute myelogenous leukemia (AML), and are therefore a subject of keen interest.
Clinker visualises such fusions for simple, quick recognition of canonical or novel forms. Clinker allows the uses the to explore the potential oncogenic fusions in IGV as well as producing publication ready figures.
A superTranscript is a novel method for constructing a transcriptome and visualising a gene. Effectively one takes all the transcript products of a gene and flattens them into an ordered single linear representation of the transcriptome. The resulting visualisation is very effective for viewing splice junctions within a gene and is hence a great tool for viewing splicing between fused genes.
Clinker creates superTranscripts through combining the coding sequences of the two genes identified by fusion finders to form a superTranscriptome.
Wow... Fine. Have a look at a BCR-ABL1 fusion. The purple line indicates the fusion splice junctions.
Run through the pipeline with our tutorials and generate your own BCR:ABL1 image. Or visit the running the pipeline page for a breakdown on how the various stages in the pipeline works.