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 -
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.
Dept. of Bioinformatics and Genomics, UNCC
North Carolina Research Campus
600 Laureate Way
Kannapolis, NC 28081
From: galaxy-user-bounces(a)lists.bx.psu.edu on behalf of Jeremy Goecks
Sent: Thu 7/8/2010 5:06 PM
To: Michael Yourshaw
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)
You can view BAM files on the UCSC genome browser by opening a BAM dataset and clicking on
the "display at UCSC main" link.