What Does That Mean That Structural Variation Happened In Negative Strand

Question

[Chen Sun]

I have a file of structural variation information of donor genome to hg19 reference genome. The information is like this:

17      1104685548616   assembly_comparison_inversion   5886015 5886567 .       -       .       .
17      1104685270005   assembly_comparison_inversion   43210707        43211858        .       +       .       .
17      1104685351393   assembly_comparison_inversion   58198056        58201613        .       +       .       .
17      1104685350756   assembly_comparison_inversion   60646046        60646518        .       +       .       .

the 7-th column indicate whether the SV event happend in positive strand or negative strand. As you can see this is inversion event, and I want to put these events back into hg19 reference genome to reconstruct donor genome.

What I do not understand is how could SV events just happend in one single strand? and how to locate the event site if it happened in negative strand?

Answer 1

[Brad Chapman]

For flattened representations. you need to combine multiple lines in the BED file to reconstruct the full event. The BED file describes the identified breakpoints and then you combine these into the complex structural variation event. I found this review by Aaron Quinlan and Ira Hall super helpful for understanding the representations and different cases, especially figure 2:

http://faculty.virginia.edu/irahall/support/webpdfs/Characterizing_Tren_Gen2012.pdf

It took me a bit of practice to begin to see the events. My best suggestion is to draw out the breakpoints on paper until they become second nature. Hope this helps.

[Chen Sun]

Thank you for your information, while my question is that I do not understand why SV can only happen in a single strand(positive strand or negative strand). And also the reference has only a single strand, so I do not know how to put these SV back.