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 <hard-length-constraints>.
- 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.