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3.0 years ago
sumitguptabt
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30
I have mapped the UUIDs to TCGA barcode using TCGAutils, however, I got some unexplained barcode such as
UUID (Associated Barcode)
3d50d8ca-cabd-4129-80b9-ff1e84c190e5 (CPT0051690007)
54b12749-b94c-4284-a44b-ee890084141b (CPT0069370006)
543965fe-03ea-4cf3-8766-b4c4c8e168ef (HCM-CSHL-0058-C34-85C-01R-A78N-41)
Mapped barcode file which have some strange entry UUIDstoBarcode file ( gdc portal )
Can anybody help me in decoding these strange barcodes? Thank you in advance
I am pretty sure CPT is from CPTAC, and HCM is from HCMI. Neither are TCGA projects. Btw, using barcode is not a good habit in general. I know there were a few instances of sample type updates in TCGA before. Given sample type is encoded in barcode and some of the file name, this created quite some difficulties for TCGA DCC.
Kevin Blighe would you please help?
what samples are these which tissue type?
@krushnach80 Thank you, dear, These samples are from: cancer types: bronchus and lung, subtype: adenomas and adenocarcinomas. The data is HTSeq counts from transcriptome profiling.
Hi, you can search for these here: https://portal.gdc.cancer.gov/
They seem to be from Clinical Proteomic Tumor Analysis Consortium (CPTAC)
Thank you so much Kevin Blighe I will look into it and update you ASAP. BW Sumit
You are welcome, Sumit.
Yes, indeed they are from the "Clinical Proteomic Tumor Analysis Consortium". I downloaded the metadata and it helped me. Thanks Sumit
Please don't tag individual users requesting their attention unless you're asking a question on packages they designed.
Yeah sure, dear. It was my first question and thought that it may bring immediate attention. Although latter I resolved this issue myself by downloading the metadata using payload and API. I appreciate your help and guidance. Thank you Sumit
Please avoid terms like "dear". This is a formal, professional setting and these words are of a more personal/intimate nature.