CPTAC has provided the Genomic Data Commons (GDC) with genomic data from cancer patients with diverse disease types including Uterine Corpus Endometrial Carcinoma (UCEC), Clear Cell Renal Cell Carc
Data from molecular characterization of 574 Diffuse Large B-Cell Lymphoma (DLBCL) biopsy samples is now available in the GDC Data Portal.
The NCI's Genomic Data Commons (GDC) released a new slide image viewing feature in the GDC Data Portal allowing researchers to view, zoom, and pan slide
The Querying and Downloading Data using the GDC Data Portal and the GDC Data Transfer Tool webinar will help introduce users to the GDC tools for downloading and retrieving data from cancer genomic
BAI files are included with the download when using the GDC Data Transfer Tool to download BAM files.
When using the API to download BAM files, BAI files will only be included if the related_files=true parameter is specified together with the BAM UUID, for example:
https://api.gdc.cancer.gov/data/53f4ad60-0777-409c-a34d-ca4442dc9c44?related_files=true
The Navigating the GDC - A Case Study webinar is the first webinar in a series of NCI GDC Webinar.
The file detail page and the metadata files accessible from that page (if available) can be used to determine the difference between files that share the same filename. For example, the files may be associated with different aliquots, or different patients.
Raw sequencing files submitted to the GDC are processed using GDC Genomic Data Alignment pipelines. The processed data are made available in the GDC Data Portal as BAM files containing aligned reads and unmapped reads (if available). No reads are hard-clipped, but reads that were flagged as "failed" during an Illumina sequencing run are discarded.
Harmonized BAM files from RNA-seq and DNA-seq experiments will contain both mapped and unmapped reads, if available. Unmapped reads are not distributed separately.
Capture kit information is provided by the GDC API at the read group level, where available. In some cases, additional information may be available in SRA XML files.
The relevant read_group properties returned by the GDC API are:
