GDC data available as open-access data can be used with proper accreditation. Use of controlled-access data requires dbGaP access and users must abide by the data use agreement (DUA) associated with the study. See GDC Data Access and Sharing Policies or contact the NCI Office of Data Sharing directly for further clarification: NCIOfficeofDataSharing@mail.nih.gov.
If you are interested in using the stranded data in STAR Count gene expression output, you can make a guess by comparing N_ambiguous: if a stranded type has a much lower number of N_ambiguous compared to the other stranded type and the unstranded count, it is a good indicator of a stranded library being used. Please note that knowing a library is prepared by a stranded-enabled RNA-Seq kit does not necessarily guarantee the resulting library is stranded. In addition, data of different strandness can not be compared to each other directly.
The GDC RNA-Seq workflow generates STAR counts in three different modes: unstranded, stranded_first, and stranded_second. The GDC then uses the unstranded counts as the major output for following-up FPKM and TPM normalizations to facilitate cross-project comparisons of different strandness.
FMI has provided the Genomic Data Commons (GDC) with genomic profiling data from approximately 18,000 adult patients with a diverse array of cancers that underwent genomic profilin
The Navigating the GDC - A Case Study webinar is the first webinar in a series of NCI GDC Webinar.
The NCI announced a collaboration with the Multiple Myeloma Research Foundation (MMRF) to integrate MMRF's wealth of genomic and clinical data on the disease
The NCI’s Genomic Data Commons (GDC) was officially launched on June 6th at the 2016 American Society of Clinical Oncology (ASCO) Annual Meeting by Vice President Joe Biden as part of the National
