With inSite you can:
- compare multiple genomic regions in a single view
- view binding sites/motifs that have a "type" (ie. type of transcription factor) via color
- view binding site/motif strength values via bar height
- view additional annotations as landmarks along the regions
DEMO VIDEO COMING...
SETTING COLORS The site types are initially assigned a color of gray, which you can change by clicking and dragging one of the color-squares into the legend over top of the type's associated rectangle. To remove the color, just click, drag, and release the color-rectangle somewhere outside of the legend. Colors can also be transfered from one type to another by clicking and dragging.
ADD | REMOVE | REORDER To add and remove regions and types, click on the triangles next to the labels next to the region and type labels --- then click on the region/type you want to add or remove. To reorder the regions and types, right click on the region/type to highlight it in red, then reorder using the up and down arrow keys. Click the triangles again to hide the dropdown boxes.
NORMALIZATION The default in inSite is to normalize the bar heights (ie. strength values) on a per type basis. Normalization across all binding sites is also an option. To switch to global normalization, include the optional flag below in the config.txt. file -- also optional is to specify what the minimum value should be:
NORMALIZATION: global
GLOBAL_MIN_VALUE: put your value here
SCREEN SHOT shift+P will give you a screen shot in .pdf format in the same directory as the app -- multiple screen shots can be taken during a single session. The image is saved as vector graphics so you can edit it in programs like Illustrator.
EXAMPLE DATA I've included some sample data in the download. The data files (should be, I hope!) self-explanatory. They are in .csv format, and thus human-readable in Excel or any text editor. If you look at dsim.csv you'll see examples of the "annotations" that show up as tick marks beneath the regions. Setting the lenght of an annotation to zero gives just a tick line; setting it to something greater than zero makes it span the distance. "##" indicates a comment line.