Analyze Data

HTSeq had been the default RNA-Seq expression quantification tool since the first GDC data release. The GDC later updated the RNA-Seq alignment and quantification workflow to include STAR Count, which generates stranded counts by default in addition to the existing unstranded counts. During Data Release 32 for gene model updates, the GDC had 1) augmented the existing STAR Count output to include FPKM and FPKM-UQ normalizations; 2) reprocessed all the TCGA data using the latest RNA-Seq workflow with STAR Count.

For the reference genome, the GDC has been using an augmented version of GRCh38.p2 (with additional decoy sequences and virus sequences) since inception. The GDC does not use alternative contigs, and only derives high-level data from the major chromosomes, so the same reference genome is used for both gene model GENCODE v22 (from Data Release 1 to 31) and GENCODE v36 (from Data Release 32). As future versions of the reference genome are released, e.g., GRCh39, the GDC will evaluate the benefits of updating data to utilize the new version.

There is a variety of target capture kits used by different sequencing centers. Most of the whole exome capture kits share many common genomic regions, especially for cancer related genes; However, which exons are included is totally dependent on the vendor's library preparation kit. There are often more differences among capture regions from different Targeted-Sequencing/Panel data.

The GDC does not perform batch effect corrections across samples for the following reasons:

A recent data release offers new ways to access data from the Count Me In project.

Target capture kits are used to "target" specific regions of a given genome for the Whole Exome Sequencing (WXS) and Targeted Sequencing experimental strategies. Users should therefore take care when comparing data from different target capture kits for the WXS and Targeted Sequencing experimental strategies because of potential differences in genomic regions targeted, variant filtering, and subsequent variants recovered.

The GDC’s Data Release 26 features updates allowing Multiple Myeloma Research Foundation (MMRF) CoMMpass data to be explored directly in the GDC Data Portal.

In a major update to GDC's Data Portal, users can now plot and explore clinical data in the Analysis area.

Users who have been granted access to Foundation Medicine data can now visualize somatic mutations using GDC Data Analysis, Visualization, and Exploration (DAVE) tools.

The GDC released a new version of the GDC Data Portal with new visualization tools for copy number variations (CNVs).