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  • brachysclereid
    Member
    • Feb 2011
    • 32
    #1

    Replacing FASTA headers for TopHat & Cufflinks

    Hi,

    Does anyone know how to replace all the headers in a FASTA file with new names given in another list? The FASTA headers in the genome file are very complex. In the gtf file it just says scaffold1, scaffold2, etc. I need to replace each complex name with the corresponding simple name.

    Any tools out there?
    Tags: None
  • maubp
    Peter (Biopython etc)
    • Jul 2009
    • 1544
    #2
    It sounds like a straight forward scripting task - can you program in Perl, Python, Ruby, ...?

    Comment

    • brachysclereid
      Member
      • Feb 2011
      • 32
      #3
      programming

      Thanks,
      I was able to solve this problem. I am starting to program. For common tasks like this I just assumed there would be some little program already out there.

      Comment

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