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Comment pointing to Affymetrix forums has been removed from the add artefact page.
2010-01-04 21:26:07 UTC by sgblanch
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Some older versions of IGB had problems computing font metrics on certain platforms. This has been fixed in later versions.
Version 6.1 will colour the nucleotide sequence if every nucleotide is represented by at least one pixel allowing users to visualise the sequence at lower zoom levels. You need zoom in 100 percent to see the actual nucleotides. Please let us know if you do not see the...
2010-01-04 21:07:14 UTC by sgblanch
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Dear Sirs, i am using the version 5 of IGB to analyze some tiling array and deep sequencing data and i have a problem when i try to visualize the nucleotide that correspond to a particular position of the genome. As you can see in the attach document, the number of letters (nucleotides) between 1 and 20 is 16. I have downloaded the version 6.1 and now i can see different colours but not the...
2010-01-04 20:37:36 UTC by nobody
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I am a bit embarassed to admit that BAM is a new format for me. But it appears very well-documented.
Could you check in some sample files to Genoviz? (Small ones please!)
2010-01-04 18:58:17 UTC by loraine
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The version of Xerces used by IGB 5.12 was incompatible with Java 6. If you are able, you should upgrade to the latest version of IGB.
The currently available version of IGB from sourceforge is 6.0. Version 6.1 is in testing and is available via Java WebStart via http://igb.bioviz.org/.
2010-01-04 17:51:37 UTC by sgblanch
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Running Ubuntu 9.10 with Sun's Java 1.6.0_15. As soon as IGB loads, I get the following pop-up error message: (The complete Java console output is also attached)
Could not create plugin 'Data Access'.
java.lang.InstantiationException: Could not instantiate plugin
class name: 'com.affymetrix.igb.view.DataLoadView'
Caused by:
java.lang.AbstractMethodError...
2010-01-04 17:35:12 UTC by nobody
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Would be fantastic to be able to visualize stacked alignments from say BAM files loaded locally or from the DAS/2 ( http://samtools.sourceforge.net/). SNP/INDEL/ rearrangement calling would be very well assisted with this feature. It probably shouldn't be part of the track view but available under say a version of the slice view.
2010-01-04 17:31:23 UTC by biotelerock
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Provide DAS/2 distribution of sliced BAM sequence alignment files. http://samtools.sourceforge.net/.
2010-01-04 17:27:29 UTC by biotelerock
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To repeat:
Add gene model annotations and tiling array data sets from a das2 site as follows:
Launch IGB, choose Arabidopsis thaliana genome version A_thaliana_Jun_2009
Open Bioviz (Quickload) and click TAIR9 mRNA and choose Whole Genome load mode
Under Data Access tab, click Configure.
Add DAS2 site http://demodas.transvar.org/das2/genome (to get some tiling array data sets)
Choose...
2010-01-04 06:06:11 UTC by loraine
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Right-clicking a tier lab and choosing the "show all types" option causes IGB to zoom out so that the entire chromosome is in view.
2010-01-04 05:53:35 UTC by loraine
