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.
Access Data
What is the difference between files that have the same filename?
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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?
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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?
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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
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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?
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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.
How do I obtain access to a specific controlled dataset?
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The GDC provides access to both open and controlled datasets. To access controlled datasets, users must obtain appropriate authorization through dbGaP. See Obtaining Access to Controlled Data for instructions on applying for access through dbGaP.
What web browsers are supported by the GDC?
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The following web browsers are supported for use with the GDC Data Portal, Submission Portal, Website, and Documentation site.
- Most recent supported stable version of Microsoft Edge
- Most recent stable version of Google Chrome
- Most recent stable version of Mozilla Firefox
I only see patients with ages of 90 years or less in the GDC. Why is this?
Submitted by Anonymous
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HIPAA guidelines require that patients with ages greater than 89 years be aggregated into a single age category. This is to limit the ability to positively identify these individuals. In practice this will impact the values reported in several fields. We have chosen to accurately display the age at diagnosis, but fields that give dates or time periods after this benchmark may be compressed. This may include such fields as "Days to last follow up", "Days to last known disease status", "Days to recurrence", "Days to death", and "Year of death".
Why are some harmonized data files missing?
Submitted by Anonymous
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The GDC processes data through several harmonization pipelines. If the process of harmonization reveals issues in the underlying data or if an error occurred during harmonization, the harmonized data files (e.g. BAMs or VCFs) will not appear in GDC data access tools.