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Old 06-20-2008, 10:05 AM   #1
Nix
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Default Plug for new ChIP-Seq Package and the Integrated Genome Browser

Hello Folks,

Wanted to point folks running chIP-seq analysis to http://sourceforge.net/projects/useq/ . Be sure to hit the 'Project Web Site' button for more information. It contains 25+ command line java applications for both low and high level analysis. We have developed several statistics to minimize false positives using control input data and assign confidence in the peaks via empirical FDRs, binomial p-values and q-values.

Also wanted to recommend folks check out the Integrated Genome Browser and it's use of DAS/2 for distributing public/ private chIP-seq data. It's the only viable solution I've so far encountered. See http://bioserver.hci.utah.edu/BioInf...p/Software:IGB .

-cheers, David
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Old 08-05-2009, 05:13 PM   #2
ewilbanks
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Default Re: Plug for new ChIP-Seq Package and the Integrated Genome Browser

Looks great! Quick question, does your platform support analysis for any organism with a sequenced genome? Or is it restricted to commonly used systems (human, mouse, etc...)?

Thanks!
Lizzy

Last edited by ewilbanks; 08-05-2009 at 05:14 PM. Reason: typo
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Old 08-06-2009, 06:39 AM   #3
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IGB has been in development for 10+ years and is one of the better genome browsers out there.

It supports many reference genomes through the DAS/2 protocol and there are several options for creating your own.

Ann Loraine's group at UNC has picked up spearheading its development after Affymetrix released it as open source.

Get the latest info and release from http://igb.bioviz.org/

In my opinion, IGB is the best browser for working with high throughput genomic datasets. We have adopted it for our Core facility and release all of our analysis (RNA-Seq, chIP-seq, SNP discovery, gene expression microarray...) using the public/ private Genoviz DAS/2 server.
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Old 08-12-2009, 10:31 AM   #4
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Hi, Nix,

I downloaded USeq, but got java.lang.UnsupportedClassVersionError. My java version is 1.5.0_12. Can I recompile USeq to solve this problem? If so, how can I do that?

Thanks
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Old 08-12-2009, 11:26 AM   #5
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Thanks!

Sorry if my question was confusing, I was actually referring to your ChIPseq peak calling algorithm in the USeq package. Are there any species restrictions in terms of the genomes that can be used with this?

Thanks again!
Lizzy
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Old 08-12-2009, 01:24 PM   #6
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There are a couple classes that require java 1.6 for the GUI.jar to compile. You could delete these and make an attempt. The source is in the download. Otherwise, upgrade your java to 1.6.

As far as species restrictions, no, USeq is agnostic, there are several places where the apps want a species genome build name (e.g. H_sapiens_Mar_2006). This is inserted into the bar graph files and will instruct DAS aware browsers what genome to load the files into. Otherwise its not used.

-cheers, D
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Old 08-12-2009, 01:25 PM   #7
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awesome thanks!
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