Segway Heat map of parameters

Question

[christoph.neu]

Hello,

I want to discover chromatin patterns in ChipSeq data using segway. I followed the quick start instruction and trained a model on the test dataset.

wget http://noble.gs.washington.edu/proj/segway/2011/test.genomedata
segway train test.genomedata traindir
segway identify test.genomedata traindir identifydir

Now, I would like to know which patterns are enriched in a given state (Similar to Fig1 in the tools publication or ChromHMM's emission parameters heatmaps.)

I can not find any mentioning of it in its documentation

Thanks.

Answer 1

[christoph.neu]

For future reference (The segway mailing list helped out):

To generate heatmaps, you should use the segtools software suite (https://hoffmanlab.org/proj/segtools/). Specifically you want to look at the command, segtools-gmtk-parameters, which will generate a heatmap of emission parameters from the trained Segway model (yourtraindirectory/params/params.params).