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:
- Bowtie (Manual and Source available from here)
- Human genome in fasta format (Download hg19.2bit from here)
- Cutadapt (Manual and installation instructions are detailed here)
- Trim galore (Perl script is available here)
- Bismark (Excellent resource is available here)
- Methylkit (useful R package for downstream analysis on this google code page)
- Install all the above scripts/programs in the directories in your PATH or export it.