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From Jie Wu Home Page

Revision as of 20:56, 8 April 2013 by Wuj (Talk | contribs)

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Contents

  • 1 Programs about mRNA-seq
    • 1.1 QC
    • 1.2 Mapping
    • 1.3 Processing
    • 1.4 Quantification
    • 1.5 Differential expression
  • 2 Useful websites about splicing
  • 3 Communities

Programs about mRNA-seq

I only listed programs I use regularly, for a more complete list, please check [[1]].

QC

  • FastQC

Mapping

  • Bowtie
  • BWA
  • OLego
  • TopHat
  • MapSplice
  • PASSion
  • GSNAP

Processing

  • SAMtools
  • BEDtools
  • HTseq-count

Quantification

  • Cufflinks
  • Scripture
  • SpliceTrap

Differential expression

  • Cuffdiff
  • DESeq
  • DEXseq

Useful websites about splicing

  • RNAinfo, A website about RNA
  • ESEfinder
  • SFmap

Communities

  • SEQanswers
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