Manny's Bioinformatics Workshop

Manny's workshop:

• Introduction to Linux
  • Recommended software
    • Windows machines: MobaXterm
    • Apple machines: Xquartz
  • Linux notes
  • ppt
  • Alan's information about the Cluster Using the cluster
  • Alan's information about how to use SLURM Using SLURM
  • More notes on shell scripts and writing SLURM batch files More Slurm

• Introduction to Sequence Technology
  • ppt (updated Aug 22, 2014)
  • Fastx toolkit
  • Fastqc

• Introduction to Sequence Alignment
  • ppt
  • Blast notes
  • Bowtie notes
  • Samtools
  • MUMmer

• SNP analysis
  • Using mpileup on Samtools
  • Running samtools mpileup mpileup notes
  • Preparing files for GATK and running GATK GATK notes
  • Getting snps from a specific region VCF region

• Visualizing your alignments
  • IGVnotes

• Introduction to Mapping and Sequence Assembly
  • ppt
  • Velvet Documentation
  • ABySS

• Introduction to RNA-seq
  • ppt
  • Bowtie2
  • Tophat
  • Cufflinks
  • CuffDiff
  • DESeq manual

Manny's R Lectures:

• R Objects and Read/Write Files
  • ppt
  • Exercise 1
  • Worksheet 1
  • example.txt
  • example.csv

• Writing Functions in R
  • ppt
  • Normalized Data
  • Worksheet 2
  • genes5expvalues

• Introduction to Statistics
  • ppt

• Plotting using R
  • ppt
  • breast cancer dataset
  • Worksheet 3
  • Volcano plot

• Data cleaning and working with packages
  • Next-gen workflow
  • Bioconductor
  • Example file
  • Clean SNP data
  • Convert SNP File format

• Differential Gene Expression using DESeq
  • RNA-seq
  • DESeq

• Clustering and GeneSet Enrichment analysis
  • ppt
  • Clustering
  • Loading Phytozome data
  • Notes to convert Phytozome Data to GOStats