Breakdancer SV Questions

[palldredge]

These might be very simple questions, but I am new to looking at breakdancer output files, and I am having a little trouble interpreting orientation of some of the SVs. I looked at the examples in the readme and also a few previous posts on this forum, but I am still confused. Can anyone offer some insight?

Is this a correct interpretation for the example below?

At locus 1 there are 40 discordant reads on the + strand and 0 discordant reads on the minus strand.
At locus 2 there are 0 discordant reads on the + strand and 40 discordant reads on the – strand.
Of all those discordant reads at both locations, there are 40 discordant read pairs that support the translocation. The orientation would therefore be +/-

Locus 1 40+0-
Locus 2 0+40-
CTX -150
99 40

But, how do I interpret orientation when I have something like the following?

For example:

Locus 1 3+8-
Locus 2 16+12-
ITX 4262
62 2

OR

Locus 1 45+7-
Locus 2 46+21-
ITX 46745
99 22

Thanks in advance!

[ernfrid]

You're interpreting the output correctly and, as you've noticed, you can't deduce orientation. If your prediction assembles then you can use the resulting contig to determine orientation, but it is impossible to determine from breakdancer output alone.