Question: Need help with "Map with Bowtie for Illumina" tool
gravatar for ghliu83
4.5 years ago by
United States
ghliu830 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
ADD COMMENTlink modified 4.5 years ago by Jennifer Hillman Jackson25k • written 4.5 years ago by ghliu830
gravatar for Jennifer Hillman Jackson
4.5 years ago by
United States
Jennifer Hillman Jackson25k wrote:


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:

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

Best, Jen, Galaxy team

ADD COMMENTlink written 4.5 years ago by Jennifer Hillman Jackson25k
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