Recount2 TCGA metadata missing sample, run and experiment columns
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@mariela-cortes-lopez-15111
Last seen 3.1 years ago
IMB, Mainz

Hi,

I'm working with junction data recovered from snaptron, which uses recount data. I want to obtain the metadata information of each sample but I can not find the matching sample number in the recount TCGA metadata object recovered with the function:

all_metadata("tcga")

In fact, the columns  "sample", "experiment"  and  "run" in the metadata object only have "NA" values. Is this some kind of error in the metadata object? 

The recount version that I'm using is  1.2.3

Thanks

recount metadata tcga • 404 views
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@lcolladotor
Last seen 12 days ago
United States

Hi,

TCGA is not part of SRA, or at least wasn't when recount2 was made. Use the TCGA-specific ids for matching samples there such as gdc_file_id instead of run.

Best, Leonardo

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