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Clinker is a bioinformatics pipeline that generates a superTranscriptome from popular fusion finder outputs (JAFFA, tophatFusion, SOAP, deFUSE, Pizzly, etc), that can be then be either viewed in genome viewers such as IGV or through the included plotting feature developed with GViz.
Genomic structural abnormalities, such as the translocation between and within chromosomes, is common in cancer and can result in the fusion of two genes which then function as an oncogenic driver. Such fusion genes are therefore indicative of cancers such as Chronic Myelogenous Leukaemia (CML), Acute Lymphoblastic Leukaemia (ALL) and Acute Myelogenous Leukaemia (AML), and are therefore a subject of keen interest.
The output from Clinker will allow a user, through IGV or the customised Gviz plot, to quickly recognise canonical or novel forms and produce them as a publication ready figure.
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 fusion genes.
The Clinker pipeline creates superTranscripts through combining the coding sequences of the two genes identified by fusion finders to form a superTranscriptome, which it then aligns to and creates custom transcript, protein and gene annotations for.
Wow... Fine. Have a look at a BCR-ABL1 fusion output created by the customised GViz script. 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.