BIOINFORMATICS AND APPLICATIONS BIO 4033/ BIO 5033

Bioinformatics part I

• 1. Multiple Sequence Alignments
  • 1.1. Getting started with MEGA
    • 1.1.1. How to make an alignment using MEGA
    • 1.1.2. Edit the alignments
    • 1.1.3. Exporting MSA
• 2. Steps of building a tree
  • 2.1. Make multiple sequence alignment for Globin gene family
  • 2.2. Find informative sites for Parsimony
  • 2.3. Building Phylogenetic trees
• 3. Steps of building a tree (Part II)
  • 3.1. Make multiple sequence alignment for Globin gene family
  • 3.2. Find the best substitution model
  • 3.3. Building Phylogenetic trees

High-throughput data analysis

• FastQC analysis using Cyverse Discovery Environment (DE)
  • Step 1: Login into Cyverse DE
  • Step 2: Getting data into Cyverse Discovery Environment
    • URLs
  • Step 3: Performing FastQC analysis:
  • Reference:
• Relaunching a stalled analysis in Cyverse Discovery Environment
  • Step 1: Click on the message icon
  • Step 2: Click on the analysis that appears to be stalled
  • Step 3: Check the small box and click on analysis
  • Step 4: Click on the relaunch button
• Adapter and quality trimming using trim-galore
  • Step 1: Launching Trim-galore
  • Step 2: Selecting output folder
  • Step 3: Selecting input files
• Mapping short reads
  • Step 1: Mapping with Tophat2
  • Step 2: Mapping with Bowtie2
• Counting mapped reads
• Differential gene expression analysis
  • DESeq tutorial:
  • Steps to perform DEseq analysis
  • DE gene list

Protein analysis

• Secondary Structure Prediction
• Tertiary Structure Prediction

qPCR data analysis

• The Delta-Delta Ct Method
  • Normalization
  • Average of the control samples (normal cells)
  • Calculate the ∆∆Ct relative to the average of ∆Ct normal cells
  • Fold gene expression for each sample
  • Overall fold change
  • Log transformation
  • T-test

Galaxy for HTS analysis

• Getting data into Galaxy
  • Step 1: Login into Galaxy
  • Step 2: Getting data
  • Step 1: Click on the upload icon on upper left hand corner
  • Step 2: Copy one of the links above. Click on the Paste/Fetch icon and paste link in the box. Click on start.
  • Step 3: One the data is uploaded, they will appear in the right hand panel. You can use the pencil icon to change the name.
  • |Reference:
• FastQC analysis using Galaxy
  • Step 1: Login into Galaxy
  • Step 3: Performing FastQC analysis:
• Adapter and quality trimming using Cutadapt
  • Step 1: Launching Cutadapt and performing the analysis
• Adapter and quality trimming using trim-galore
  • Step 1: Launching Trim-galore
  • Step 2: Selecting input files
  • Step 3: Advance settings
• Use Splice aware aligner, Tophat2 to align short reads
  • Output files:
• 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/))
  • Windows
  • If you already have R and RStudio installed
  • If you don’t have R and RStudio installed
  • macOS
  • If you already have R and RStudio installed
  • If you don’t have R and RStudio installed
• 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

Indices and tables

• Index
• Module Index
• Search Page