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  • 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?

  • #2
    It sounds like a straight forward scripting task - can you program in Perl, Python, Ruby, ...?

    Comment


    • #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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