Bioinformatics targeted workshops

Introduction to Illumina Genome and RNASeq Data Analysis

  • Designing and making the libraries
  • Sequencing platforms (MiSeq, HiSeq, NextSeq), multiplexing
  • What Illumina data looks like
  • Processing (quality evaluation, cleaning, trimming)

De‐novo transcriptome RNASeq assembly from with Trinity

  • Expected knowledge:
    • Using Linux in Bioinformatics
    • Introduction to Illumina Genome and RNASeq Data Analysis
  • De‐novo vs. on‐genome assembly
  • Running Trinity pipeline
  • Assembly quality assessment
  • Detection of coding regions with TransDecoder
  • Transcriptome functional annotation with Trinotate

RNASeq based gene expression and co‐expression analysis

  • Expected knowledge:
    • Introduction to Illumina RNASeq Data Analysis
    • Introduction to programming in R
  • How to design and execute RNASeq based gene expression analysis project
  • Mapping of RNASeq reads on genome or transcriptome
  • Gene differential analysis using Tuxedo protocol
  • Gene co‐expression analysis with WGCNA

Variant calling from with GATK and FreeBayes

  • Expected knowledge:
    • Using Linux in Bioinformatics
    • Introduction to Illumina Genome and RNASeq Data Analysis
  • Exome vs Whole genome
  • Data preparation
  • Read mapping
  • SAM format explained
  • samtools and picard toolkits
  • GATK pipeline step‐by‐step
  • VCF format explained - vcftools toolkit
  • FreeBayes

De‐novo genome Illumina and PacBio assembly

  • Expected knowledge:
    • Using Linux in Bioinformatics
    • Introduction to Illumina Genome and RNASeq Data Analysis
  • What to choose and why: Illumina, PacBio or hybrid?
  • Illumina PE and MP libraries
  • PacBio reads
  • Illumina assembly with SPAdes, SOAPdenowo and SGA
  • PacBio SMRT pipeline and HGAP3 assembly
  • PBJelly – joining PacBio and Illumina datasets