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Question: Need help with "Map with Bowtie for Illumina" tool
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gravatar for ghliu83
4.5 years ago by
ghliu83 • 0
United States
ghliu83 • 0 wrote:

Hi, I mapped my illumina sequences with one reference bacterial genome and got bam file. Does any guy know what tool I should use to visualize the alignment? And need tutorial for step-by-step bacterial genome alignment or assembly. Thanks. 
tool bowtie • 1.6k views
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modified 4.5 years ago by Jennifer Hillman Jackson ♦ 25k • written 4.5 years ago by ghliu83 • 0
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gravatar for Jennifer Hillman Jackson
4.5 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

You can visualize the data using Trackster inside of Galaxy. If you mapped using a built-in genome to Galaxy, there will be a small stacked bar graph icon for your dataset that you can click on to launch the tool, or click on the top menu bar for "Visualization". If you mapped as a Custom Reference Genome, add the .fasta file (same as used for mapping), as a Build under the top "User" menu, then use that in Trackster as the reference. 

This wiki link shows where the tutorials and other learning resources from our community are located:
https://wiki.galaxyproject.org/Support#Learning_Hub

For genome assembly, a local or cloud Galaxy with tools from the Tool Shed (if those of interest are available) will be needed.

http://getgalaxy.org or http://usegalaxy.org/cloud
http://usegalaxy.org/toolshed

Best, Jen, Galaxy team
ADD COMMENT • link written 4.5 years ago by Jennifer Hillman Jackson ♦ 25k
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