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  • Trouble in converting UCSC transcripts IDs

    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

  • #2
    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.

    Comment


    • #3
      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.

      Comment


      • #4
        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?

        Comment


        • #5
          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
          Last edited by watermark; 04-16-2014, 08:13 AM.

          Comment


          • #6
            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).

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

            Comment


            • #7
              Thanks Genomax, it was helpful.

              Comment


              • #8
                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 ?

                Originally posted by GenoMax View Post
                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).

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

                Comment


                • #9
                  Originally posted by watermark View Post
                  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

                  Comment

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