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  • cuffdiff: extract gene info from chr coordinates

    Hi,

    Cuffdiff output (gene_exp.txt) has chromosome coordinates. What is the quick way to get gene information?

    the output has gene names, but some genes don't have gene names. So chromosome coordinates are probably the only way. I didn't think those XLOC IDs are useful for that.

  • #2
    If you are working with a genome that is available in Ensembl then using the BioMart tool would be a simple way to get the gene information. http://www.ensembl.org/biomart/martview

    You should be able to do something similar with the Table Browser in UCSC genome browser. http://genome.ucsc.edu/cgi-bin/hgTables?command=start

    Comment


    • #3
      Thank you GenoMax. That works.

      Is there a way to do that in batch mode?

      Originally posted by GenoMax View Post
      If you are working with a genome that is available in Ensembl then using the BioMart tool would be a simple way to get the gene information. http://www.ensembl.org/biomart/martview

      You should be able to do something similar with the Table Browser in UCSC genome browser. http://genome.ucsc.edu/cgi-bin/hgTables?command=start

      Comment


      • #4
        Originally posted by JQL View Post

        Is there a way to do that in batch mode?
        You can do BioMart queries through their API. See more info here: http://www.biomart.org/martservice.html

        Comment

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