I'm doing a project and want to to visualize the variants' locations on the MexR gene for Pseudomonas Aeruginosa and create plots showing the distribution of predicted functional impacts. I'm a beginner and was recommended to use IGV but I don't know how to do this.
1 answer
Here is a good IGV tutorial: https://training.galaxyproject.org/training-material/topics/introduction/tutorials/igv-introduction/tutorial.html
Specifically for your task at hand, you need to get an annotated genome of Pseudomonas Aeruginosa from NCBI genbank. Download the gbk (genbank file format). Then you need to find the variants of interest, usually these are in vcf file format. Add both of these as tracks in IGV.
Good luck.
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