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From the main window of IGV, click on File -> Import Genome... and you should be presented with the following window.
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From the main window of IGV, click on File -> Load from File.... Choose bowtie.sorted.bam
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There are a lot of things you can do in IGV. Here are a few:
- Zoom in using the slider in the upper right. So this until you see reads.
- Navigate by clicking and dragging in the window. This is how you move left and right along the genome.
- Navigate more quickly. Use
page-uppage-down,home,end. - Jump to the next point of interest. Click on a track name on the left side of the window (Ex: bowtie.vcf), to select it. You can then use
control-fandcontrol-bto jump forward and backward within that list of features. Try this on the variant calls track. - Jump right to a gene. (If you have gene features loaded.) Type its name into the search box. Try "topA".
- Load multiple BAM alignments or VCF files at once. Try this to compare a few different regions between the bowtie and BWA results.
- Change the appearance of genes. Right click on the gene track and try "expanded". Experiment with the other options.
- Change the appearance of reads. Right click on a BAM track and choose "show all bases" and "expanded". Experiment with the other options.
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