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  • Mark
    Member
    • Nov 2008
    • 54
    #1

    tophat accepted_hits.sam file

    Hi All

    When running tophat v1.0.10 with the --GFF flag, the accepted_hits.sam file produced is empty (though the .expr file is seemingly correct). Without the --GFF flag it produces a correct accepted_hits.sam file. This does not seem to be proper behavior. Any ideas what's going on? Thanks.
    Tags: None
    • sdriscoll
      I like code
      • Sep 2009
      • 436
      #2
      are you positive your GFF file is produced correctly? before i had a proper GFF file for my organism tophat produced questionable results when using the --GFF flag.
      /* Shawn Driscoll, Gene Expression Laboratory, Pfaff
      Salk Institute for Biological Studies, La Jolla, CA, USA */

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