Mapping files to patients in TCGA (RNA-seq)

Question

[Roza]

Hello & good day,

I need help regarding downloading TCGA (RNA-seq) dataset. I have no idea about Bioinformatics, my background is computer science. I would like to run this code. I'm trying to run the code provided here: https://github.com/luisvalesilva/multisurv/blob/master/data/preprocess_omics.ipynb

I have an issue in mapping files to patient via cases.0.submitter_id.

When I downloaded RNA-seq from the manifest provided by the author gdc_manifest.2019-08-23.txt, the mapping process failed, I think due to changes that occurred in the gdc portal. So what I did is, I downloaded the updated version of RNA-seq from gcd, then when I map files to patients, I was able to map only around 1000+ patients whereas around 8000+ couldn't.

Could you guide me how to handle this?

Does that means only around 1000 patients RNA-seq are publicly available (access control = open)?

Your help is much appreciated.

Thank you

[Zhenyu Zhang]

Not sure about the particular notebook you mentioned. But in general, once you added these files to GDC cart, there is a sample_sheet you can download from the cart. This sample sheet TSV file contains the exact file to patient mapping you are asking for.

[Roza]

Thank you Zhenyu Zhang, I wasn't aware about this (sample_sheet).

Answer 1

[Ming Tommy Tang]

you may want to take a look at https://bioconductor.org/packages/release/bioc/html/RTCGA.html or https://bioconductor.org/packages/release/bioc/html/TCGAbiolinks.html

[Roza]

thank you Ming Tang