Trouble in converting UCSC transcripts IDs

[watermark]

Hi all,

I have downloaded data from TCGA. it's RNAseqv2 gene expression data. I have gene ID and isoforms(transcripts) of the genes which are from UCSC.
I want to convert them to Refseq transcript ID or Entrez transcript ID. I used Biomart but it failed. does anyone knows how to handel this ?


Here is the IDs of some of my isoforms:

uc011lsn.1
uc010unu.1
uc010uoa.1
uc002bgz.2
uc001jiu.2

[GenoMax]

You can use the table browser from UCSC to get the data you need: http://genome.ucsc.edu/cgi-bin/hgTables?command=start

Use the right genome/build for the data. You can then use the "identifiers" button to paste in your list of id's.

[watermark]

Yes, I tried it, but I couldn't find the hits.
I use genome version hg19, human. the ID which I pase is human transcripts from TCGA.

[GenoMax]

I recollect that we had a previous discussion about this where I had posted a link to the file that had the mapping info: https://webshare.bioinf.unc.edu/publ...ownToLocus.txt

It appears that you are now looking at some isoforms that did not have corresponding name in the file. Is that correct?

[watermark]

Basically what I want to do is to convert this isoform IDs(transcript ID) to the transcript ID in the TargetScan.

More percisly I want to map the isforms IDs from TCGA to IDs like :

Transcript ID in TargetScan
NM_130786
NM_130786
NM_130786
NM_130786
NM_130786


TCGA Transcript ID:
uc001udr.2

[GenoMax]

Download the file here: http://hgdownload.soe.ucsc.edu/golde...oRefSeq.txt.gz

You should be able to grep out the id's from the file (the number at the end may be different than the one you have, I think that is the version number).

$ grep "uc001udr." knownToRefSeq.txt
uc001udr.3      NM_001243014

[watermark]

Thanks Genomax, it was helpful.

[watermark]

what is the knownToRefSeq ? it's basically are all transcript(isoforms) which are known ? so I will miss lots of the isforms when I'm converitng ?

Download the file here: http://hgdownload.soe.ucsc.edu/golde...oRefSeq.txt.gz

You should be able to grep out the id's from the file (the number at the end may be different than the one you have, I think that is the version number).

$ grep "uc001udr." knownToRefSeq.txt
uc001udr.3      NM_001243014

[GenoMax]

what is the knownToRefSeq ? it's basically are all transcript(isoforms) which are known ? so I will miss lots of the isforms when I'm converitng ?

knownToRefSeq will relate the NM_* and NR_* names to UCSC gene names uc0*

See Hiram Clawson's (UCSC support) answer in this thread: http://redmine.soe.ucsc.edu/forum/in...01fe5506a9f16c