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Old 08-18-2010, 10:58 AM   #1
Siva
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Location: Ames, IA

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Default 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 at 08:40 PM. Reason: Clarity
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Old 08-18-2010, 12:07 PM   #2
quinlana
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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.

Aaron
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Old 08-18-2010, 12:10 PM   #3
quinlana
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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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