Assemble

In a nutshell

The ASSEMBLE functions post-process individual cMonkey2 runs. These steps include:

• GRE discovery by TOMTOM
• Genome-wide GRE scanning by FIMO
• Aggregation of all ensemble info into MongoDB
• Corem detection

These tools return a MongoDB database that can be queried by the QUERY functions

Requirements

For these scripts to work, you will need:

• Access to a cluster running the SGE scheduler
• A completed cMonkey2 ensemble (see BUILD documentation)

in addition to the system requirements listed in this documentation

Tutorial

If you meet all of the requirements and are ready to ASSEMBLE an ensemble, continue to our Assemble Tutorial.

MongoDB Database Schema

The MongoDB Database Schema is available here