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1. Become comfortable with the basic steps of indexing a reference genome, mapping reads, and converting output to SAM/BAM format for downstream analysis.
2. Use bowtie2 to map reads from an E. coli Illumina data set to a reference genome and compare the output.

Theory

Please see the Introduction the Introduction to mapping presentation on presentation on the course outline for more details of the theory behind read mapping algorithms and critical considerations for using these tools and references correctly.

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• In the bowtie2 example, we mapped in --local mode. Try mapping in --end-to-end mode (aka global mode).

• Do the BWA tutorial so you can compare their outputs (note BWA has a conda package making it even easier to try).
  • Did bowtie2 or BWA map more reads?
  • In our examples, we mapped in paired-end mode. Try to figure out how to map the reads in single-end mode and create this output.
  • Which aligner took less time to run? Are there any options you can change that:
    • Lead to a larger percentage of the reads being mapped? (increase sensitivity)
    • Speed up run time without causing many fewer reads to be mapped? (increase performance)

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