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  • David Lyon
    Member
    • May 2010
    • 11

    #1

    gff to refFlat

    I am looking to convert gff files to refFlat

    does anyone have any scripts I can use to do this conversion?

    Thanks
  • marcora
    Member
    • Jan 2010
    • 52

    #2
    Do you mean refFlat to GFF?

    Comment

    • btuser
      Junior Member
      • Sep 2010
      • 3

      #3
      Do you know of any script that I can use to convert refFlat to GFF3 or raw juncs format for use with TopHat?

      Comment

      • marcora
        Member
        • Jan 2010
        • 52

        #4
        Originally posted by btuser View Post
        Do you know of any script that I can use to convert refFlat to GFF3 or raw juncs format for use with TopHat?
        Download refFlat in GTF format from UCSC and then convert to GFF3 using the script found here:

        Discussion of next-gen sequencing related bioinformatics: resources, algorithms, open source efforts, etc

        Comment

        • btuser
          Junior Member
          • Sep 2010
          • 3

          #5
          Thank you!

          Comment

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