extract TCGA barcodes and sample_type information from uuids
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gv ▴ 40
@gv-6516
Last seen 22 months ago
United States

Hi,

I have a list of fileuuids obtained from TCGA portal. I am trying to use GenomicDataCommons package to extract sample type(whether normal or tumor) and TCGA barcodes associated with input fileuuids. From the manual I can get to this

resp = cases() %>% filter(~ project.project_id=='TCGA-LUAD') %>%
  GenomicDataCommons::select(c(default_fields(cases()),'samples.sample_type')) %>%
  response_all()

Can someone guide me how to extract TCGA barcode and sample type from list of uuids?

Thanks

GenomicDataCommons R • 269 views
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@kevin
Last seen 5 hours ago
Republic of Ireland

The answer can be found via Sean Davis: GenomicDataCommons Example: UUID to TCGA and TARGET Barcode Translation. Note that, once you infer the barcode from the UUID, you can then infer tumour|normal from the barcode.

Kevin

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HI Kevin, I used Sean's code and got the barcodes. How can I infer tumor|normal from them? For example if I have these barcodes:

TCGA-05-4249-01A
TCGA-05-4250-10A
TCGA-05-4382-01A
TCGA-05-4390-10A
TCGA-05-4395-01A

Thanks

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Ah, for that, please take a look here: https://www.biostars.org/p/313063/

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Hi Kevin Blighe Sean Davis , the link is really helpful to do the translation, and I found TCGAutils is helpful too.

But, I got a question. As below, "afe6dd5c-a32e-4ba8-a9b5-154b27a9513b" is the file_id. How about the prefix in the bam file or bai file? What id it is?

ls afe6dd5c-a32e-4ba8-a9b5-154b27a9513b
f689d486-2605-4110-946e-4b8831aa2f3d_gdc_realn_rehead.bai  f689d486-2605-4110-946e-4b8831aa2f3d_gdc_realn_rehead.bam  logs
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