Question: Which version of UCSC annotation are used in TCGA RNASeqV2 isoforms expression data ?
0
gravatar for jack
6.0 years ago by
jack800
Germany
jack800 wrote:

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 ?

 

 

ADD COMMENTlink modified 2.7 years ago by -_-850 • written 6.0 years ago by jack800
1
gravatar for mazur
5.7 years ago by
mazur10
Germany
mazur10 wrote:

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

ADD COMMENTlink written 5.7 years ago by mazur10
1

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?

ADD REPLYlink written 3.8 years ago by sumithra.das10

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

ADD REPLYlink written 3.8 years ago by namshik.han0

Hi Johanna,

This GAF file is perfect!

Cheers

 

 

ADD REPLYlink written 5.3 years ago by Jonathan Crowther200
0
gravatar for -_-
2.7 years ago by
-_-850
Canada
-_-850 wrote:

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

ADD COMMENTlink written 2.7 years ago by -_-850

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

ADD REPLYlink written 2.7 years ago by genomax83k
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