Some users have reported problems getting data to display in IGB after opening a file or accessing a data server. If you are having problems, read on. If none of the suggestions listed below help, please contact us for assistance.trouble viewing your data, see:
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Check that your file is in a format we support
IGB can open and read nearly all of the common data and graph files used with genomics data. For more information about supported file types, please see File Formats. We also take requests - if you would like us most formats commonly used in genomics.
See File Formats.
If you would like IGB to support a new type of file format, please let us know.
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Click Load Data button
IGB allows you to open files from your desktop, local servers, URLs or other data sources. This can be done through File>Open, or by simply dragging and dropping the file or URL into the IGB display. However, if the file contains a lot of data, IGB will not instantly start loading the data into the displaycan open and display data files located on your computer, Web sites, and Quickload sites.
When you first open filesa file, IGB adds them it to the list of opened files in the Load Mode table Data Management table in the Data Access tab. . The Data Management table lists a Load Mode for each opened file. By default, IGB adds most files and data sets using the Region in View Manual load mode setting, which means you must manually trigger data loading. To display load data from these filesa resource with Load Mode setting of Manual, zoom in to a region you want to see, and click the Refresh Load Data button . Whatever data located in the file that overlaps with the current region in view will appear in the display.If your data file is not large, it's probably best to set the Load Mode to Whole Genome. If you do that, IGB will load all the data right away. top right of the main IGB window.
Tip: Change Load Mode to Genome to trigger loading all the data at once. Only do this for smaller data sets.
Examples of data sets that work best when loaded in the Whole Genome mode include: gene models for the entire human genome or the junctions.bed file created by the TopHat spliced alignment program.
For more about loading files, please see Loading Data.
.bam files need a .bai file
IGB can readily display alignments data from .bam files. However, it requires a .bam index file (called a .bai) to be present in the same folder as the .bam file. For more about creating .bam and .bai files, please see Making BAM Files for IGB (RNA-Seq)
- List of significant regions identified in a ChIP-Seq experiment
- GTF files output from CuffLinks
- T-DNA insertion lines (Arabidopsis)
See Loading data.
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I opened my sequence file
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but all I see is a gray bar and dashes.
When you open a "fasta" (or other sequence) file, and if you have not already selected a species and genome, then IGB will read the file and construct a new genome, using the names of the sequences it finds in the file.
However, to To save memory, IGB doesn't load sequence data until you click the Refresh Data Load Sequence button. To view the bases, click the Refresh Data button Load Sequence button and then zoom in.
If you have opened a sequence file, but not refreshed it, when you zoom in you will see a gray bar with dashes, indicating the sequence bases has not yet been added to the display.
If you have already refreshed your data, then when you zoom in for a closer look, you'll see color-coded sequence bases. By default, IGB uses warmer colors to represent G's and C's and cooler colors to depict A's and T's. You can change the color scheme if you like by choose File->Preferences->Other Options.
For more about zooming, please see Zooming and Scrolling.