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XiaoTaoWang / NeoLoopFinder

A computation framework for genome-wide detection of enhancer-hijacking events from chromatin interaction data in re-arranged genomes
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How to plot region not in assembly #54

Open Josephinedh opened 1 year ago

Josephinedh commented 1 year ago

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 commented 11 months ago

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

C42B-ETV1

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 commented 11 months ago

In the specific case you provided, can you try

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