<![CDATA[BOL: HOMER: Software for motif discovery and next-gen sequencing analysis]]> https://bioinformaticsonline.com/bookmarks/view/27078/homer-software-for-motif-discovery-and-next-gen-sequencing-analysis? https://bioinformaticsonline.com/bookmarks/view/27078/homer-software-for-motif-discovery-and-next-gen-sequencing-analysis Tue, 26 Apr 2016 03:48:23 -0500 https://bioinformaticsonline.com/bookmarks/view/27078/homer-software-for-motif-discovery-and-next-gen-sequencing-analysis <![CDATA[HOMER: Software for motif discovery and next-gen 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


RNA-Seq

  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)


Microarray

  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.

Address of the bookmark: http://homer.salk.edu/homer/basicTutorial/

]]> Neel