Hi-Culfite Processing Pipeline
JuiceMe is heavily based on the Juicer pipeline. Please review the Juicer documentation first to understand how the JuiceMe pipeline works.
In addition to the Juicer dependencies, you will need:
- bwa-meth
- Samtools
- Python
- MethylDackel
Be sure to download the latest Juicer Tools jar and to put the MethylDackel executable in the scripts directory.
You will also need to create index files using bwa-meth and put these in your references directory.
Otherwise, the pipeline proceeds as described in the Juicer documentation and the setup is the same.
Python scripts for the various methylation analyses are included in the Analysis folder.