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  • biofreak
    Member
    • Jun 2011
    • 44
    #1

    makeTranscriptDbFromUCSC

    I have used the following command:
    txdb <- makeTranscriptDbFromUCSC(genome = "canFam2", tablename = "refGene")
    Does anyone know how to modify values in txdb object?
    I want to change the chromosome names in particular.
    thanks
    Tags: None
    • colindaven
      Senior Member
      • Oct 2008
      • 417
      #2
      Nope. I had to change my sequence fasta files to get to the correct chromosome names in my alignment (since I'm repeatedly aligning to that reference.).

      A quicker way around might be to use the Unix command sed on your SAM files.

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