There are many reason that If you are having trouble viewing your data might not be visible, but let's start with the most common reasons:
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, see:
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Check that your file is in a format we support
IGB can utilize nearly all of the common data and graph files used with genomics data. However, .sam files and a few others will not work with IGB. For more information about supported file types, and converting to recognized file types, please see File Formats.
Refresh your data
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 of choice. However, IGB do NOT instantly open these files. Often times, files are very large, there is a long list of the files you would like to see or internet service can be laggy. After adding files to IGB, they can be seen in the Chose load mode list in the center of the Data Access panel. At this point you must refresh to see the data. You can set the individual files to load only the Region in View (zoom in to a specific region or gene) or you can set it to Whole Chromosome which will load the entire sequence, be it a chromosome, or a contig, etc. You can then either refresh one file/track at a time using the symbol next to the track name or you can load everything at once by using the Refresh Data button. For more about loading files, please see Loading and Sharing Data.
.bam files need a .bai file
IGB can readily display .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).
.bnib and .fa (FASTA) files appear as a gray bar
IGB shows sequence as a gray bar when zoomed all the way out. As you zoom in onto smaller and smaller segments of the sequence, the gray bar will pop into color and finally color with the actual sequence present. If you have loaded your sequence data, but not refreshed it, it will remain gray with dashes, indicating the data has not yet been loaded. For more about zooming, please see Zooming and Scrollingopen and read most formats commonly used in genomics.
See File Formats.
If you would like IGB to support a new format, let us know.
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Click Load Data button
IGB can open and display data files located on your computer, Web sites, and Quickload sites.
When you first open a file, IGB adds it to the 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 Manual load mode setting, which means you must manually trigger data loading. To load data from a resource with Load Mode setting of Manual, zoom in to a region and click the Load Data button located in the 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 Genome mode include:
- 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 but all I see is a gray bar and dashes.
To save memory, IGB doesn't load sequence data until you click the Load Sequence button. To view the bases, click the Load Sequence button and then zoom in.