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Throughout the course we have focused on aligning a single sample of reads against a single reference genome with a few exceptions, but sometimes we know that is not the biological case. Sometimes we know that there are multiple different things present in a single sample. Most common situation would be a sample with a chromosome as well as a plasmid. Here we will examine the same sample used in the novel DNA identification tutorial to see how inclusion of the 2nd reference file changes the mapping results.
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The discussion of concepts in this tutorial are identical to the advanced mapping with bowtie2 tutorial and work with the same data. The commands in this tutorial will take ~15 minutes. Discussion of results is more thorough in the advanced mapping tutorial. As that tutorial directly assess the difference between multiple mapping types. |
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- Does it effect the mutations that are called?
- Does it effect the percent of reads mapped as was observed in the advanced mapping tutorial?