How to plot region not in assembly

[Josephinedh]

Hi,

Thank you for a very nice package.

I've been trying to use the plotting functions to create figures of regions that aren't detected in the assembly. However, I'm not sure what to write in the last two columns, such as "8,126710000" and "8,127685000" in this example:

C0 duplication,8,126680000,-,8,127765000,+ 8,126710000 8,127685000

I couldn't figure out what these two columns are besides being close to the SV region, can you please help me figure out what I should write here to make the plot?

Thanks,
Josephine

[XiaoTaoWang]

Hi Josephine,

Sorry for the late response. The last two columns indicate the coordinates of the other end of the first and the last fragments that will be plotted. For example, the figure below corresponds to the assembly:

C1 translocation,14,37520000,+,7,14160000,+ 14,36250000 7,12480000

However, you have the flexibility to adjust the "span" parameter when you construct the Triangle object to modify the extended region for plotting.

Best,
Xiaotao

[XiaoTaoWang]

In the specific case you provided, can you try

C0 duplication,8,126680000,-,8,127765000,+ 8,126880000 8,127565000?