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  • 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.

  • #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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