October 15, 2013

Reduced Representation Bisulfie Sequencing Data Analysis

I am writing this post to help researchers trying to analyse their own RRBS data. This is non-technical explanation. Just following the steps may help on any ubuntu/linux system. Requirements on the computer:
  1. Bowtie (Manual and Source available from here)
  2. Human genome in fasta format (Download hg19.2bit from here)
  3. Cutadapt (Manual and installation instructions are detailed here)
  4. Trim galore (Perl script is available here)
  5. Bismark (Excellent resource is available here)
  6. Methylkit (useful R package for downstream analysis on this google code page)
  7. Install all the above scripts/programs in the directories in your PATH or export it.
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