Segway 2.0 Documentation

Homepage:http://pmgenomics.ca/hoffmanlab/proj/segway Author:Michael M. Hoffman <michael dot hoffman at utoronto dot ca> Organization:Princess Margaret Cancer Centre Address:Toronto Medical Discovery Tower 11-311, 101 College St, M5G 1L7, Toronto, Ontario, Canada Copyright:2009-2015 Michael M. Hoffman Last updated:July 14, 2017

For a conceptual overview see the paper:

Michael M. Hoffman, Orion J. Buske, Zhiping Weng, Jeff A. Bilmes, William Stafford Noble. 2012. Unsupervised pattern discovery in human chromatin structure through genomic segmentation. Nat Methods 9:473-476. doi:10.1038/nmeth.1937.

Manuscript version available at PubMed Central requires no subscription.

For a preprint of a protocol on using Segway see:

Roberts EG, Mendez M, Viner C, Karimzadeh M, Chan RCW, Ancar R, Chicco D, Hesselberth JR, Kundaje A, Hoffman MM. 2016. Semi-automated genome annotation using epigenomic data and Segway. Preprint: http://doi.org/10.1101/080382

• Quickstart Guide
  • Installation and configuration
  • Acquiring data
  • Running Segway
  • Results
• Segway 2.0 Overview
  • Installation
  • The workflow
  • Data selection
  • Model generation
  • Task selection
  • Train task
  • Identify task
  • Posterior task
  • Python interface
  • Command-line usage summary
  • Environment Variables
  • Running Segway for large jobs
  • Helpful commands
• Technical matters
  • Working files
  • Temporary files
  • Distributed computing
  • Memory usage
  • Reporting
  • Performance
  • Names used by Segway
• Frequently Asked Questions
  • How do I troubleshoot errors that occur in the training or identification process?
  • How do I make segments longer?
  • How can I make Segway go faster?
• Troubleshooting
• Support