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  • mmmm
    Senior Member
    • Jul 2013
    • 131

    #1

    coveragebed_bed tools

    when using coverageBed within BedTools to identify annotated genes within reference genome (gff file) that are not covered by reads- I understand that a value of 1 indicates that that gene is fully covered by the reads however- a value of less than 1 (does it indicates low coverage?)- and what about (0), does this indicate that the region is not covered at all or there is a possiblity that it is missing from the sequenced chromosome and that's why it showed ) coverage in the reads?- how could we prove that?
  • TiborNagy
    Senior Member
    • Mar 2010
    • 329

    #2
    -counts counts the overlap and do not calculate fractions.
    You can also check the alignment with IGV.

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    • mmmm
      Senior Member
      • Jul 2013
      • 131

      #3
      thanks-
      what about coverage of (0.2) of a certain gene in relation to the reference gene- does this mean that reads covered only part of that gene??

      Comment

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