How to find out sample type information of '.rna_seq.augmented_star_gene_counts.tsv' files in TCGA?

Question

[Anamika Acharyya]

I downloaded around 900 '.rna_seq.augmented_star_gene_counts.tsv' files from TCGA using GDC manifest tool. Now I want to know the sample type information (eg., primary tumor or normal ) of each of these files. I have looked into 'Biospecimen.json' and all possible .json files for getting the sample type information. 'Biospecimen.json' has all the information about portions and aliquots but associated RNA seq file names are not there. Also, any ID that can map these RNA seq files are not present.

I found a similar question in Biostars. It goes here : how to find sample type information from TCGA?

The solutions provided here did not work for me. Please help. TIA.

[Ram]

TCGA is not specific enough as a source. You can use TCGABiolinks to download clinical and other metadata based on cohort and platform.

Answer 1

[Zhenyu Zhang]

When you added your files, there is a row of buttons in the GDC cart that you can use to download additional metadata. "sample type" is directly downloadable in the sample_sheet tsv file

Btw, this sample_type is very overloaded, and has been refactored. I think you'd better to look into tissue type, tumor descriptor, etc in the future.

[Anamika Acharyya]

Thanks a lot for the help!