Versions Compared

Key

  • This line was added.
  • This line was removed.
  • Formatting was changed.

...

Once a file is opened, IGB adds it to the Data Management Table in the Data Access tab.

Note

IGB does NOT immediately display loaded files. Many of today's next-gen sequencing files are too big to display all at once. IGB handles this issue by waiting to visualize data sets until you ask it to load data.Opening a file does not automatically cause IGB to start showing data in the file. Because some data files are very large, you must first zoom in and click the Load Data button load the data into IGB. 

...

Use Data Management Table to configure data loading settings (optional)

IGB is capable of loading and displaying whole genomes, whole chromosomes or just portions of a data file, depending on the file type. Therefore, although there are many load options, not every file type can be loaded the same way. There is always the option of Don't Load, which will simply not load the individual file but will maintain it in the list.

...

To change how and when IGB loads data into a track, open the Data Access panel and change settings under Load Mode in the Data Management Table.

Options include:

  • Don't Load means no data will load when you click the Load Data button. 
  • Genome triggers automatic loading of all data from a file.
  •  Manual means that only data overlapping for the currently displayed region will load when you click Load Data. This is the default setting for most files.
  • Auto is an option for BAM and SAM files (e.g. CoolI1T1.sm.bam), which will allow IGB to automatically load the data in view, if the view is zoomed below the Auto threshold, marked with a yellow arrow head (red arrow). The Auto zoom level can be adjusted to your needs. First, set the main view to the zoom level you want. Then, means that moving or zooming to a new location triggers data loading, but only when the zoom threshold is lower than the mark shown on the horizpontal zoomer. Change the threshold by selecting View > Set AutoLoad Threshold to Current View. This will change the needed zoom level AND will move the yellow arrow to indicate the new threshold setting. 
Warning

If you set the Autoload threshold too high, IGB will try to load all of the indicated data, which could exceed the memory limit.

 

...

Click Load Data or Load Sequence buttons

...