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Angela Matchan edited this page Jan 28, 2016
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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 (May 2016), only pipelines for mapping (with STAR), lane QC and fusion gene detection are included in this codebase but this will be added to over time with the following; differential expression, gene/transcript quantification, splice variant analysis and allele specific expression.