gene expression analysis using TopHat and Cufflinks

  1. Install latest Bowtie2. See here.
    $ bowtie2 --version
    /opt/bi/bowtie2-2.2.6/bowtie2-align-s version 2.2.6
    Built on localhost.localdomain
    Wed Jul 22 16:18:32 EDT 2015
    Compiler: gcc version 4.1.2 20080704 (Red Hat 4.1.2-54)
    Options: -O3 -m64 -msse2  -funroll-loops -g3 -DPOPCNT_CAPABILITY
    Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}
  2. Install latest TopHat. See here.
    $ tophat2 -v
    TopHat v2.1.0
  3. Install latest Cufflinks. See here.
    $ cufflinks
    cufflinks v2.2.1
    linked against Boost version 104700
  4. Prepare the reference genome. See here.
  5. Check your data
  6. Build the transcriptome index. See here.
  7. Protect your reference data.
  8. Prepare your working directory.
  9. Download data (lung).
  10. Download data (stomach).
  11. Check your data.
  12. Read alignment with TopHat.
    Map the reads for each sample to the reference genome:
  13. Quantification with Cuffquant.
    Compute the gene expression profiles which are used subsequently by Cuffdiff:
  14. Optional:
    1. Delete data.
    2. Check your data.
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