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  • Comprehensive TopHat manual?

    The manual on the website seems to leave a bit to be desired. It great for actually getting a run to produce results but does not seem to explain all the possible auxiliary scripts that may be included or explain how to process the results with much more detail than "You can load them into UCSC GBrowser".

    Do any of you know of a place that actually lists the column names/classifications for the output files?

    Thanks.

    Gus
    In science, "fact" can only mean "confirmed to such a degree that it would be perverse to withhold provisional assent." I suppose that apples might start to rise tomorrow, but the possibility does not merit equal time in physics classrooms.
    --Stephen Jay Gould

  • #2
    At the very bottom of the TopHat manual under the heading TopHat Output, links are provided to the specification of each output file.

    HTH

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