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, GTF, CSV, and JSON 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.
http://bioinf.iasi.cnr.it/tcga2bed/
ftp://bioinf.iasi.cnr.it/
Please credit TCGA2BED in your manuscript by citing:
Fabio Cumbo, Giulia Fiscon, Stefano Ceri, Marco Masseroli, and Emanuel Weitschek. "TCGA2BED: extracting, extending, integrating, and querying The Cancer Genome Atlas." BMC Bioinformatics (2017) 18 1:6. https://dx.doi.org/10.1186/s12859-016-1419-5