MethylCoder is a single program that takes of bisulfite-treated reads and outputs per-base methylation data. It also includes scripts for analysis and visualization. In addition to a binary output and a SAM alignment file, the direct output of methylcoder is a text file that looks like
- C Compiler
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Bioinformatics. 2011 Sep 1;27(17):2435-6. doi: 10.1093/bioinformatics/btr394. Epub 2011 Jun 30.
MethylCoder: software pipeline for bisulfite-treated sequences.
Pedersen B, Hsieh TF, Ibarra C, Fischer RL.