TCGA data, relationship between different sources

Question

[9606]

I am to analyze TCGA data for RNA-Seq of many tumors.

I found that data can be downloaded either from Genomic Data Commons: https://gdc-portal.nci.nih.gov/

or from UCSC Xena:

https://xenabrowser.net/datapages/?host=https://tcga.xenahubs.net

For what it concerns RNA-Seq data, they do have some differences: for example the former uses FPKM and the latter RSEM; also UCSC Xena are further divided in RNA-Seq v1 and RNA-Seq v2.

What is the relationship between the two data sources? Is there any difference in terms of reliability?

Answer 1

[GenoMax]

I assume you are referring to the Version 1 and Version 2 RNAseq data analysis protocols that were used at UNC. You can find a document about the details of the steps used in those protocols at this link. Basically all of V1 was reprocessed using V2 and that is newer of the two protocols.

GDC has since reprocessed all data using a process that is described on this page.

To get prompt response about questions regarding GDC/TCGA data you should consider emailing GDC tech support (support at nci-gdc.datacommons.io).