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Introduction

cgpRna has been developed by the Cancer Genome Project's (CGP)-IT Group at the Wellcome Trust Sanger Institute (https://www.sanger.ac.uk/research/projects/cancergenome/) and provides pipelines, for RNA-Seq data, that implement commonly used mapping and analysis programs, such as TopHat and rna-star.

At the present time, only a fusion gene detection pipeline is included but this will be added to over time with the following; core mapping, QC, differential expression, gene/transcript quantification, splice variant analysis and allele specific expression.