Is there a way on the public Galaxy to look at read alignments in bam files (or any other format) equivalent to IGV or samtools tview? (preferably not actually using buggy tview)
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Michael Yourshaw UCLA Geffen School of Medicine Department of Human Genetics, Nelson Lab 695 Charles E Young Drive S Gonda 5554 Los Angeles CA 90095-8348 USA myourshaw@ucla.edu 970.691.8299
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Is there a way on the public Galaxy to look at read alignments in bam files (or any other format) equivalent to IGV or samtools tview? (preferably not actually using buggy tview)
Michael,
You can view BAM files on the UCSC genome browser by opening a BAM dataset and clicking on the "display at UCSC main" link.
Thanks, J.
Hello,
This may work, but I will have to test it to be sure.
You may be able to simply click-drag the "BAM" file directly from the Galaxy Web page interface into IGB 6.3 (Integrated Genome Browser - http://www.bioviz.org/igb/IGB_6.3.shtml.)
IGB is a desktop genome browser and provides access to a large number of genomes -- all the ones available at UCSC and several that aren't. It is different from UCSC and IGV in that it does animated zooming, edge matching, and a lot of other user-friendly features designed for viewing and comparing reads and annotations aligned onto a reference genome.
Anyway, if the click-dragging works, you'll see the BAM file appear in the 'Load Mode' table under the Data Access Panel in IGB.
You can then set the "Load Mode" to "Region in View", zoom in on a region using the slider or double-clicking on a feature in the dsiplay, and then click "Refresh Data" to load the reads.
-Ann
____________________ Ann Loraine Associate Professor Dept. of Bioinformatics and Genomics, UNCC North Carolina Research Campus 600 Laureate Way Kannapolis, NC 28081 704-250-5750 www.transvar.org
-----Original Message----- From: galaxy-user-bounces@lists.bx.psu.edu on behalf of Jeremy Goecks Sent: Thu 7/8/2010 5:06 PM To: Michael Yourshaw Cc: galaxy-user@bx.psu.edu Subject: Re: [galaxy-user] is there an equivalent of IGV or samtools tview?
Is there a way on the public Galaxy to look at read alignments in bam files (or any other format) equivalent to IGV or samtools tview? (preferably not actually using buggy tview)
Michael,
You can view BAM files on the UCSC genome browser by opening a BAM dataset and clicking on the "display at UCSC main" link.
Thanks, J.
galaxy-user@lists.galaxyproject.org
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Jeremy Goecks -
Loraine, Ann -
Michael Yourshaw