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Which version of UCSC annotation are used in TCGA RNASeqV2 isoforms expression data ?

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
• 9,626 views • link
updated by Ram Ram • written by jack jack

2 answers

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

• 0 views • link
written by mazur • mazur

Hi Johanna,

This GAF file is perfect!

Cheers

• 0 views • link
updated by Ram Ram • written by Jonathan Crowther Jonathan Crowther

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?

• 1 views • link
written by sumithra.das • sumithra.das

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

• 0 views • link
written by -_- -_-

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

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written by GenoMax GenoMax

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