Diffuse Large B-Cell Lymphoma Data Available in GDC Data Portal
Data from molecular characterization of 574 Diffuse Large B-Cell Lymphoma (DLBCL) biopsy samples is now available in the GDC Data Portal.
Access Data
The NCI GDC Releases New Slide Image Viewer
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
GDC Webinar: Querying and Downloading Data using the GDC Data Portal and the GDC Data Transfer Tool
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
How can I download BAM index files (BAI files) using the API?
Submitted by Anonymous
on
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/b0986067-67c0-40a9-afeb-264fcddebe96?related_files=true
GDC Webinar: Navigating the GDC - A Case Study
The Navigating the GDC - A Case Study webinar is the first webinar in a series of NCI GDC Webinar.
What is the difference between files that have the same filename?
Submitted by Anonymous
on
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.
How can I access GDC sequencing data in FASTQ format?
Submitted by Anonymous
on
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.
Are unmapped reads available in the GDC Data Portal?
Submitted by Anonymous
on
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.
Where can I find the target and bait/probe files (BED files) that describe the capture kit used in an exome sequencing experiment?
Submitted by Anonymous
on
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:
How do I avoid timeouts and transfer interruptions when downloading large datasets from the GDC Data Portal?
Submitted by Anonymous
on
The GDC Data Portal is a web-based application that is limited by browser and network constraints. If a system timeout occurs when downloading files, please use the GDC Data Transfer Tool or contact the GDC Help Desk.