GDC Data Query

Question

[p20170409]

I am working on the GDC TCGA cancer data specifically for miRNA and lncRNA. The aim of my study is to identify the interaction between lncRNA and miRNA in various cancer types.

For my research purpose, I had downloaded the RNAseq and miRNAseq data from TCGA-GDC for all cancer using the TCGA and GDC command-line script. I am facing some issues with the data so I need some clarification.

1. How many lncRNA data are there in TCGA GDC because after downloading the lncRNA data using the GDC client I am getting the same set of lncRNA for each cancer type. My question is whether all lncRNA is actively present in all cancer types and in all the patients, or there is something wrong with the data.

   1. Regarding miRNA data for TCGA-OV, TCGA-PAAD, and TCGA-UCS I am getting the same set of miRNA count, Is there any other way I can get hold of that data. can I get access to that data from some other source?

Answer 1

[Zhenyu Zhang]

are you complaining about getting full matrix data instead of truncated data? btw, for TCGA data in GDC, better to specify if it's legacy archive data or active portal data