MIA-View

Overview

MIA-View is a portable program used to visualize multiplex genomics data, such as SPRITE, ChIA-Drop, PoreC, etc. These are visualized with an interactive incidence matrix, allowing for seamless zoom & pan. For more detailed documentation on CLI tool usage and build systems, see docs/.

Installation

For Windows, download and run the corresponding .exe file. For linux, download the .deb file and run

sudo dpkg -i miaview-1.0-linux-x64.deb
sudo ln -sf /opt/miaview/bin/miaview /usr/local/bin/miaview

miaview # Run

For MacOS,

• download and open the .dpm file. Drag miaview into applications to install the program.
• Attempt to run the program. (it will not run immediately due to Mac security issues)
• Open Settings > Privacy & Security. Scroll down to "miaview" was blocked to protect your Mac and click Open Anyway.
• Now run the program again. If another menu shows up, click Open Anyway again and enter your password.

Tutorial

Loading Data

The program will first prompt for a reference genome. For our example data, select hg38.

To load multiplex data, press + below the chromosome axes and select Incidence Track to open the data selection menu.

Before displaying data, we need to perform preprocessing. In the drop-down, select the type of data. For our example data, select gemline. Then select Load new dataset....

Click Browse... to browse for raw data. For our example data, browse for GM12878-CTCF-pooled_comp_FDR_0.2_PASS.gemline. Then select Load dataset and wait until it completes.

Upon completion, click Close.

The dataset should now appear in the data selection menu. Make sure it is selected and click Select.

After some time, the data should be loaded.

Mouse Controls

• Use the mouse wheel to zoom in/out, and use shift + mouse wheel to pan left/right.
• Use the left mouse button to drag over regions of interest. After dragging, press Zoom to go to that region. Multiple regions may be selected.
• Use the right mouse button to open a menu with more advanced options.

Keyboard Shortcuts

• Undo a search with ctrl+Z. Redo with ctrl+shift+Z.
• Increase resolution with PgUp. Decrease resolution with PgDn.

References

TODO

Citation

TODO

For questions or bug reports, contact Joseph (jacjosep@umich.edu) or visit the "Issues" page.