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Snowflake Yeast Alignment

Instructions

Create a excercise/{user}/wk06/README.md. Use this to keep track of your commands and present your results. Use the read files in ~/share/OMICS/wk06/reads.

  • Sub-sample the first 100K from each set into a new file in your working directory. Remember to keep track of sample names and R1/R2s.
  • Use bwa mem to align these reads to the SGD genome.
  • Use samtools view to determine how many reads aligned from each sample at a Q30 threshold. Create a table in your README describing this.
  • Use samtools depth and determine the average depth across each chromosome in each sample.
  • After alignment, sorting, and indexing, download them to your own computer and load them into IGV.
  • Use the IGV browser, find a region where there seems to be a amino-acid change between the three samples. Take a screenshot and add it to the Readme.
  • Do a brief search about the protein, is anything known? Write about it in the README.