How can I import TARGET data into RStudio?
Hi! I saw a similar post with my question (https://support.terra.bio/hc/en-us/community/posts/360073223011-How-can-I-get-TCGA-data-into-the-notebooks-for-analysis-? ), but it doesn't fully solve my issue.
1. I need to make my own 'copy' of the Terra-hosted dataset to my bucket to access it? I just want to make sure that I understand this point correctly.
2. I ran this workflow (https://anvil.terra.bio/#workspaces/broad-firecloud-tcga/TARGET_AML_hg38_OpenAccess_GDCDR-12-0_DATA/workflows/broadinstitute_cga/gdc_file_downloader__RNAseq__HTSeqCounts__gene_expression_quantification__txt__cfg) to export the RNAseq count matrix of TARGET_AML dataset, but it failed. It's somewhat cumbersome to find the error message, which is still not informative enough to resolve my issue. Here is the stderr:
Traceback (most recent call last):
File "/opt/src/disk_size_calculator.py", line 71, in <module>
main()
File "/opt/src/disk_size_calculator.py", line 51, in main
file_metadata=file_metadata_retriever.get_metadata(file_uuid)
File "/opt/src/disk_size_calculator.py", line 26, in get_metadata
return responseDict['data']
KeyError: 'data'
Could you help me to resolve this issue? Thanks!
- Sehyun
Comments
1 comment
Hi Sehyun Oh,
Unfortunately, TARGET workspaces on Terra are no longer being maintained by the Broad Data Sciences Platform (DSP). Our advice would be to download the data directly from GDC: https://ocg.cancer.gov/data/data-access.
Please let me know if you have any other questions.
Best,
Samantha
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