Which version of UCSC annotation are used in TCGA RNASeqV2 isoforms expression data ?
2
0
Entering edit mode
10.3 years ago
jack ▴ 980

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 • 8.7k views
ADD COMMENT
1
Entering edit mode
10.1 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

ADD COMMENT
1
Entering edit mode

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 REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

Hi Johanna,

This GAF file is perfect!

Cheers

ADD REPLY
0
Entering edit mode
7.0 years ago
-_- ★ 1.1k

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 COMMENT
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 1213 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6