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  • Wei-HD
    Member
    • Oct 2009
    • 59
    #1

    Data txt file

    Hi All,

    I want to ask a very basic question concerning the input file format for Tophat and Cufflinks.

    My data file is txt file and Fastq format. But where I should start for using Tophat, should I just upload the txt file?

    Thanks in advance!

    Wei
    Last edited by Wei-HD; 01-21-2010, 04:20 AM.
    Tags: None
  • Xi Wang
    Senior Member
    • Oct 2009
    • 317
    #2
    Fastq format is ok for tophat. Refer to the tophat manual. Cufflinks uses the output of tophat as input.
    Xi Wang

    Comment

    • Wei-HD
      Member
      • Oct 2009
      • 59
      #3
      Thanks Xi!
      I read the manual, the test_data has .fq suffix, could I use .txt file directly?

      Comment

      • Jonathan
        Member
        • Jun 2009
        • 36
        #4
        Usually, yes. If it complains, just rename the file and rerun.
        -Jonathan

        Comment

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