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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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.
AaronLeave a comment:
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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
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