Trying To Visualize 2 Bam Files From Galaxy

Question: Trying To Visualize 2 Bam Files From Galaxy

5.2 years ago by

Ben Gift • 10 wrote:

I'm trying to start a visualizer with two different files to show a person where the variants are. Can I start IGV or something like it with multiple files? I read the docs and didn't find anything about it. I also asked here http://www.biostars.org/p/82032/

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modified 5.2 years ago by Vosberg, Sebastian • 30 • written 5.2 years ago by Ben Gift • 10

5.2 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hi Ben, You can launch Trackster (the Galaxy native "Visualization") directly from one dataset, then add in any other dataset from any of your histories or from Shared Libraries. Or, you can start the Visualization directly without any datasets, and later add datasets in all at once, or in increments. Make sure to "save" if you decide to navigate away while it is indexing (if the datasets are very large/numerous). Other display options appear within expanded dataset as lines like "display in IGB Local Web". You can click on multiple datasets and they should all load into the same session at the remote host. As noted in the Biostar post, datasets can also just be added to many external vis tools. But the above are the ones integrated. Hopefully this helps, Jen Galaxy team -- Jennifer Hillman-Jackson http://galaxyproject.org

ADD COMMENT • link written 5.2 years ago by Jennifer Hillman Jackson ♦ 25k

5.2 years ago by

Vosberg, Sebastian • 30

Vosberg, Sebastian • 30 wrote:

Hi, just download the IGV binary distribution from the Broad's website, unpack and start the appropriate file (it depends on your OS, explained in the readme). Then. in Galaxy, open the BAM file by clicking on "display with IGV LOCAL". Each BAM file will be loaded into the same window of IGV. Alternatively, download the BAMs, open the IGV and load files locally from your PC. Best, Sebastian Helmholtz Zentrum München LMU München mail: sebastian.vosberg@helmholtz-muenchen.de sebastian.vosberg@med.uni-muenchen.de ________________________________________ To: galaxy-user@lists.bx.psu.edu Subject: [galaxy-user] Trying to visualize 2 bam files from Galaxy I'm trying to start a visualizer with two different files to show a person where the variants are. Can I start IGV or something like it with multiple files? I read the docs and didn't find anything about it. I also asked here http://www.biostars.org/p/82032/ Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH) Ingolstädter Landstr. 1 85764 Neuherberg www.helmholtz-muenchen.de Aufsichtsratsvorsitzende: MinDir´in Bärbel Brumme-Bothe Geschäftsführer: Prof. Dr. Günther Wess Dr. Nikolaus Blum Dr. Alfons Enhsen Registergericht: Amtsgericht München HRB 6466 USt-IdNr: DE 129521671

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