Meaning letters in TCGA sample barcode field
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22 days ago
sumitguptabt ▴ 20

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

GDC Barcode TCGA • 622 views
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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.

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Kevin Blighe would you please help?

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what samples are these which tissue type?

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@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.

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Hi, you can search for these here: https://portal.gdc.cancer.gov/

They seem to be from Clinical Proteomic Tumor Analysis Consortium (CPTAC)

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Thank you so much Kevin Blighe I will look into it and update you ASAP. BW Sumit

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You are welcome, Sumit.

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Yes, indeed they are from the "Clinical Proteomic Tumor Analysis Consortium". I downloaded the metadata and it helped me. Thanks Sumit

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Please don't tag individual users requesting their attention unless you're asking a question on packages they designed.

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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

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Please avoid terms like "dear". This is a formal, professional setting and these words are of a more personal/intimate nature.

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