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Old 07-28-2009, 09:34 PM   #1
baohua100
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Default wig file for genome browser

We have Solexa RNA-Seq data and alignment results. And Populus genome sequence and GFF files.

Now we want to view the genome (gene model) and alignment data on our local computer. How can we setup the system?

Last edited by baohua100; 07-28-2009 at 09:52 PM.
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Old 07-29-2009, 08:04 AM   #2
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I'd recommend IGB. It's well suited to this task. http://igb.bioviz.org/ Also look at the USeq tools for converting your RNA-Seq alignment data into a better track visualization (see the ReadCoverage, PointDataManipulator, and ScanSeqs apps). http://useq.sourceforge.net
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Old 07-29-2009, 09:18 PM   #3
apratap
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Hi All

It is something exactly what I am also looking for. Thanks baohua for raising this question. I have heard people at gmod community are also adapting Gbrowse for visualizing short reads.

It would be great if you can share any other browsers which are out there.

Thanks,
-Abhi
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Old 07-29-2009, 09:27 PM   #4
baohua100
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Can we setup a UCSC genome broswer in local computer for this task?
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Old 07-30-2009, 06:39 AM   #5
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There's a better way for distributing your genomic data using the DAS/2 protocol (http://www.biodas.org). If you have some familiarity with the command line you can set up your own DAS/2 server (http://bioserver.hci.utah.edu/BioInf.../Software:DAS2). This version enables public private data resource distribution and works in tandem with IGB and other DAS/2 enabled browsers such as Gbrowse. Shortly (in the next 3 months) we'll be releasing a Flex Web GUI driven DAS/2 server with a relational database back end that even a bench scientist can use to publish their data.

Here's a teaser:

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