Course Curriculum (Online Bioinformatics)

Hourly timeline

 

DISCLAIMER: This can not be applied and should not be applied to patient data

 

9 – 9:15 am Introduction to the course

  • 5 Minute Goals for this course and Expectations
  • 5 minutes Next 2 days, what will we cover course content
  • 5 minutes, Software we will be using for this course
9:15-10:15 am RNA-seq pipeline Part1

  • Data pipeline overview (5 mins)
  • Quality Control (20 minutes)
    • Phred scores
    • Fastqc software
  • Downloading/uploading Fastq files (15 minutes) Practical
  • Loading Genome Space, Galaxy and Gene Pattern software and running Fastqc on a real Fastq file (20 minutes)
10:15 – 10:30 am Break for Coffee
10:30 am – 11:00 am Aligning data to a reference genome (Theory)

  • What is alignment (5 mins)
  • STAR and Tophat aligner (10 mins)
  • Software on GenomeSpace (10 mins)
  • Reference sequence (Fasta) (5 mins)
11:00 – 11:45 David’s lecture on Sequencing technologies
11:45 am – 12:45 pm Lunch Break
12:45 – 1:45 pm RNA-seq pipeline Part2 : Alignment on Galaxy server (Vishal)

  • Introduction to available parameters for alignment (10 mins)
  • Perform alignment (10 mins)
  • Discuss output files (10 mins)
  • Converting Sam to Bam via Samtools (30 mins)
  • Picard Tools
1:45 – 2:45 pm Basic Stats (mean, testing and statistical power, P-value) Ben’s lecture
2:45-3:00 pm Break for coffee
3 – 3:45 pm Normalization of data and Read counting(Vishal)

  • RPM / RPKM normalization (5 mins)
  • DESEQ normalization (15 minutes)
  • Counting reads using HT-seq  (20 mins)
3:45-4:00 Break
4 – 5 pm Running HTSeq-count (Vishal)

  • Clustering for a better Idea (15 mins)
  • Demo for htseq-count (20 mins)
  • Joining Counts from HTseq (10 mins)
  • Wrap up and what’s next tomorrow (10 mins)

 

Day 2

9-10 am Gene Pattern / Galaxy and Differential Expression

  • DESEQ2 for differential Expression (55 mins)
10 -11 am Gene set enrichment analysis online using GSEA and DAVID (Mark), Paid vs Free options: Paid: Basespace, QLUcore.com, Ingenuity pathway
11am – 11:15 am Break with Coffee
11:15 am – 12 pm ChIP-seq analysis with peak calling (Vishal)

  • ChIP-seq introduction (20 min)
  • ChIP-seq peak calling example in CISTrome (20 min)
12-1:30 Lunch Break (Conference room unavailable)
1:30-2:30 Downloading of data from open source data from Genome Browser, Data browsing via Cancer Browser, TCGA, GEO, CGA, CBIO portal (Mark)
2:30-2:45 pm Break for coffee
3 – 4 pm Variant calling (MuTect2)
4-5 pm
Machine Learning Fundamentals

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