Question: GDC data only cancer sample without normal sample
gravatar for bharata1803
11 months ago by
bharata1803240 wrote:


I want to ask about data published in TCGA and now is hosted by GDC data portal. The link is this: LINK. After I check the manifest of the metadata, there are no normal samples. Am I right? I am afraid I made a mistake and if there are no normal sample, where I can download the normal sample? Thank you.

rna-seq tcga • 330 views
ADD COMMENTlink modified 3 months ago by cindy.perscheid90 • written 11 months ago by bharata1803240
gravatar for cindy.perscheid
3 months ago by
Hasso Plattner Institute, Potsdam, Germany
cindy.perscheid90 wrote:

Hi bharata, maybe a bit late, but the there exist normal samples in the TCGA data. Not for all studies, though (e.g. not for LAML), but you can use R libraries like TCGAbiolinks to download a customized TCGA data set, e.g. with only normal samples, by specifying the sample type. Have a look here:

By the way, the sample type is also encoded directly into the TCGA barcode:



ADD COMMENTlink written 3 months ago by cindy.perscheid90

Thank you. I have solved this problem. From the new GDC portal, when we have selected all samples that we want to download, we can go to the download cart. From the download cart, we can download the samples metadata. The metadata contains a lot of information about each sample in json format. One of the information is sample type. We can also know which normal-tumor sample comes from same patient. I have written a java code to extract necessary information from the json metadata into csv format. Now, I can directly use it for downstream analysis, for example DESeq2.

ADD REPLYlink written 3 months ago by bharata1803240
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1251 users visited in the last hour