Frequently Asked Questions¶
How do I troubleshoot errors that occur in the training or identification process?¶
How do I make segments longer?¶
There are several ways to do this:
Soft weight constraints:
--segtransition-weight-scalewill increase the strength of the soft length prior for longer segments.
--prior-strengthalso does this but empirically seems to have less of an effect than
Hard weight constraints
--seg-tableoption will allow you to specify a hard minimum segment length, as described here.
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-coordsoption and supply a BED file.
Splitting up into smaller subsequences by reducing –split-sequences can also help.