Inclass Activities
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Bioinformatics part I

  • 1. Multiple Sequence Alignments
  • 2. Steps of building a tree
  • 3. Steps of building a tree (Part II)

High-throughput data analysis

  • FastQC analysis using Cyverse Discovery Environment (DE)
  • Relaunching a stalled analysis in Cyverse Discovery Environment
  • Adapter and quality trimming using trim-galore
  • Mapping short reads
  • Counting mapped reads
  • Differential gene expression analysis

Protein analysis

  • Secondary Structure Prediction
  • Tertiary Structure Prediction

qPCR data analysis

  • The Delta-Delta Ct Method

Galaxy for HTS analysis

  • Getting data into Galaxy
  • FastQC analysis using Galaxy
  • Adapter and quality trimming using Cutadapt
  • Adapter and quality trimming using trim-galore
  • Use Splice aware aligner, Tophat2 to align short reads
  • Use Htseq to counts reads mapped to features
  • Use Kellisto to map reads to cDNA and count
  • Setup instructions (This is from Data Carpentry (http://www.datacarpentry.org/R-genomics/))
  • Using DEseq and EdgeR to find differentially expressed genes
  • DEseq analysis
  • Combine DESeq and EdgR to make Venn diagram
  • GOseq analysis
  • Run RNAseq analysis as a workflow
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