Which version of UCSC annotation are used in TCGA RNASeqV2 isoforms expression data ?
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8.3 years ago
jack ▴ 940

Hi all,

I'm using TCGA RNASeqV2 expression data. They used UCSC annotation for annotating isoforms. I need to map the isoforms IDs to the RefSeq IDs, but I was able to map only 20% of them.

For this reason, I need to know, which version of UCSC annotation used for annotating RNASeqV2 data at TCGA.

Would someone help me to figure it out?

next-gen genome RNA-Seq annotation Assembly • 7.9k views
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8.1 years ago
mazur ▴ 10

Hi Jack,

I struggled today with the same problem.

I found the following file:

https://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/brca/cgcc/unc.edu/illuminahiseq_rnaseqv2/rnaseqv2/unc.edu_BRCA.IlluminaHiSeq_RNASeqV2.mage-tab.1.6.0/DESCRIPTION.txt

This file specifies the following annotation file, which was used for the RNAseqV2 TCGA-Data:

https://tcga-data.nci.nih.gov/docs/GAF/GAF.hg19.June2011.bundle/outputs/TCGA.hg19.June2011.gaf

I hope this information is of help for you.

Best,

Johanna

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Hi johanna,

The link is not accessible now as TCGA portal is no longer operational, can u tell me an alternative link to know the version of UCSC annotation used in TCGA RNASeqV2 isoforms expression data?

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Hi, You can find the file here: https://www.synapse.org/#!Synapse:syn1356421 Cheers, Namshik

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Hi Johanna,

This GAF file is perfect!

Cheers

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5.0 years ago
-_- ★ 1.0k

Here is the GDC page: https://gdc.cancer.gov/about-data/data-harmonization-and-generation/gdc-reference-files, the TCGA.hg19.June2011.gaf is the same as @namshik.han's linked file

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Moved to answer since the link is current as of Sept 2017.

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