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Old 12-22-2010, 12:38 PM   #6
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Location: US

Join Date: Jul 2010
Posts: 6

pickw please correct me if I'm wrong.

csoong, each sv call in breakdancer is decided by paired nodes. Each node contains reads within a particular region of the sequence. A particular read may support paired node 1 (ex. if has the paired reads in node 1), or it may pair up with node 2. Whenever the read does not match any when the node containing this read is trying to match another node, it will remain for the support of other nodes.

That being said, in your case, I believe the order of the first and second line being processed should be switched since it is ordered by the CHR2 and POS2 if I remember it right. Let's say

node 1 stands for chr1 809757
node 2 stands for chr12 38597387
node 3 stands for chr12 38597545

When node 1 and node 2 try to pair with each other, it finds in node 1, there are 17+ and 9- reads not paired with any other node yet, and it find 9+ reads in node 2 that can pair with node 1. So the program happily removed those 9- reads in node 1 and 9+ reads in node 2 for registration, since they already did their job.

That's why in the first line, you wouldn't see any minus strand on node 1, since they are gone to produce the second line. What about the rest of 17+ in node 1? Well, they happily paired with node 3.

Let me know if this is not clear. Thanks,
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