Quickstart Guide¶

Installation and configuration¶

With Bioconda¶

conda install segway

Generic installation¶

To install Segway first install GMTK, and install HDF5, then run this command from bash:
```
pip install segway
```
If you are using SGE, your system administrator must set up a mem_requested resource for Segway to work. This can be done by installing Segway and then running python -m segway.cluster.sge_setup.

Acquiring data¶

Observation data is stored with the genomedata system. <http://pmgenomics.ca/hoffmanlab/proj/genomedata/>. There is a small Genomedata archive for testing that comes with Segway, that is used in the below steps. You can get it using:
```
wget http://pmgenomics.ca/hoffmanlab/proj/segway/2011/test.genomedata
```

Running Segway¶

Use the segway train command to discover patterns in the test data. Here, we specify that we want Segway to discover four unique patterns:
```
segway train --num-labels=4 test.genomedata traindir
```
Use the segway identify command to create the segmentation, which partitions the genome into regions labeled with one of the four discovered patterns:
```
segway identify test.genomedata traindir identifydir
```

Note

This example spawns jobs that will run sequentially due to small segment size. See the --split-sequences option for dividing segments into smaller pieces.

Results¶

The identifydir/segway.bed.gz file has each segment as a separate line in the BED file, and can be used for further processing.
The identifydir/segway.layered.bed.gz file is designed for easier visualization on a genome browser. It has thick lines where a segment is present and thin lines where it is not. This is not as easy for a computer to parse, but it is more useful visually.
You can also perform further analysis of the segmentation and trained parameters using Segtools <http://pmgenomics.ca/hoffmanlab/proj/segtools/>.