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  • BEDTools..coverageBed query

    Hi
    I have a question regarding the way BEDtools' coverageBed handles a short read that matches both gene A and Gene B. In such an instance could you let me know which of the following is true?

    1. The read is counted for both Gene A and Gene B.

    2. The read is counted for the gene which shows lower number of mismatches.

    3. The read is thrown out.

    thanks
    Siva
    Last edited by Siva; 10-19-2010, 07:40 PM. Reason: Clarity

  • #2
    The read is counted for both gene A and gene B. You could enforce behavior #3 if you first intersected the reads against your gene file and threw away all reads having a count (-c option) > 1.

    For more complicated rules, I suggest the HTSeq package.

    Aaron

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    • #3
      You could also enforce behavior #2 by first collapsing your read alignments to the set with the lowest edit distance (NM tag if you use BAM).

      Aaron

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