FAQs

Frequently Asked Questions and Answers

• Can I specify a different Genome ID for my data if it cannot be found in the drop down in the convert-mapped-hi-c-reads-to-hic-file GUI?
  Answer
  Yes. In this updated Genomeflow, you can now supply a Genome ID if you can't find the Genome ID for your data in the GUI drop down option.

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• Can GenomeFlow show rotating/spinning 3D structure in the GUI?
  Answer
  Yes. Follow the instructions below enable rotating 3D structure in GenomeFlow GUI

1. Load the 3D structure to the GenomeFlow GUI
2. Right Click on the GUI, you will see the Spin option.
3. Browse over the Spin option and you will see on and off options.
4. Click on the on option and the 3D structure will start rotating.

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• How to save the 3D structures as rotating animations?
  Answer
  Currently, GenomeFlow can display a rotating animation 3D structure on the GUI but cannot save the rotating animation to a file.

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• How to save a video/animation showing the process of generating the 3D structure from the Hi-C data.?
  Answer
  Currently, GenomeFlow cannot save the real time video of the structure generation to file.
  My suggestion is, as a temporary but effective solution, you can record the real-time 3D structure generation by using one of the downloadable screen recording software available. The video in the link below was generated using a free Desktop screen recording software called "Free Cam" to capture the structure generation process as a video/animation file.
  Click on link to watch video

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• Why is the contact matrix file I extracted from .hic data file empty?
  Answer
  If this happens, the likely issue might be that there is no data for the normalization option selected, so it returns an empty file. Note: An important characteristic of .hic format is that it allows multiple data normalization and resolution to be stored in it.
  The solution is to select a different normalization option, and perform the extraction again