Software for motif discovery and next-gen sequencing analysis

General Next-Gen Sequencing Tutorial

This tutorial is intended to teach the basics common to most next-gen sequencing analysis.  It will cover the essential information needed to begin working with next-gen sequencing data and attempt to explain current strategies and best-practices for sequencing analysis.  This tutorial covers topics independently of HOMER, and represents knowledge which is important to know before diving head first into more advanced analysis tools such as HOMER.
  1. Setting up your computing environment
  2. Retrieving and storing sequencing files (your own data or from public sources)
  3. Checking sequence quality, trimming, general sequence manipulation
  4. Mapping reads to a reference genome
  5. Manipulating SAM/BAM alignment files
  6. Visualizing data in a genome browser


  1. De novo transcript discovery and differential analysis with Cufflinks
  2. Differential expression analysis with R/Bioconductor
  3. Clustering of large expression datasets (microarray or RNA-Seq)

  1. Basic analysis of Affymetrix Gene Expression Arrays using R/Bioconductor

General Tips for Data Analysis
  1. Excel workarounds, adding gene annotation, X-Y plots tips, etc.

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