We are maintaining an open-access ftp repository with all the public genomic and clinical data of DNA-Seq, RNA-Seq (V1 and V2), DNA-Methylation, miRNA-Seq and CNV from The Cancer Genome Atlas (TCGA) converted in BED format.
Each data set will be automatically updated when a new version of the same data set will be available on the TCGA database.
The following table shows some statistics about our public data sets.

TCGA2BED is a Java software tool that allows searching and retrieving all public genomic and clinical data of DNA-Seq, RNA-Seq (V1 and V2), DNA-Methylation, miRNA-Seq and CNV from one of the largest public repositories of cancer genomic data, The Cancer Genome Atlas (TCGA), and transforming them in standard BED format, which also allows comprehensively querying them with the GenoMetric Query Language (GMQL). A user-friendly interface is available to search, download, and convert all the public TCGA cancer related data sets.