Frequently Asked Questions

How do I troubleshoot errors that occur in the training or identification process?

See Troubleshooting and Task output.

How do I make segments longer?

There are several ways to do this:

  • Soft weight constraints:

    • --segtransition-weight-scale will increase the strength of the soft length prior for longer segments. --prior-strength also does this but empirically seems to have less of an effect than --segtransition-weight-scale

  • Hard weight constraints

    • The --seg-table option will allow you to specify a hard minimum segment length, as described here.

    • Downsampling resolution

See Segment duration model for model related methods.

How can I make Segway go faster?

  • Train on smaller portion of the genome. Use the --include-coords option and supply a BED file.

  • Splitting up into smaller subsequences by reducing –split-sequences can also help.