RNA-Seq Analysis Exercise

In this exercise, you will re-analyze the RNA-Seq reported in the following paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4224148/

  • Find the series entry on GEO.
  • You need to find out the SRR identifiers for wild type and mutant samples. For this exercise, analyzing one run from each group is sufficient.
  • Download the yeast genome fasta file and index it using bwa.
    • or, download the igenome compilation for yeast, which contains pre-indexed files.
  • Map the reads (the fastq files) against the genome file using bwa. This will give you the sam file.
  • Use featureCounts (from the subread package) to “enrich” the mapped positions in the sam file into respective gene names.
  • Compare gene counts between mutant and wild type. List 10 most different (ranked by fold-change) genes between the two groups.
1.nextgen.yeast/index.txt · Last modified: 2017/04/25 16:13 by Ahmet Sacan