BEDTools..coverageBed query

[Siva]

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

[quinlana]

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

[quinlana]

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