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RNA-seq Analysis 2014 Module 2 – Alignment and Visualization

  • Use of Bowtie/TopHat
  • ‘Regular mode’ vs. ‘Fusion mode’
  • Introduction to the BAM format
  • Basic manipulation of BAMs with samtools, etc.
  • Visualization of RNA-seq alignments - IGV
  • BAM read counting and determination of variant allele expression status