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- Main top level page for all documentation
- EnteroBase Features
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- Tutorials
- Using the API
- About the underlying pipelines and other internals
- How schemes in EnteroBase work
- FAQ
Creating a SNP Tree
Initial search
In this tutorial a tree of all predicted Salmonella typhi for samples from London will be created. First, the
initial search will be conducted in the Salmonella database. Either click on the link to "Search Strains" on
the Salmonella home page at http://enterobase.warwick.ac.uk/species/index/senterica (or if you are already on the
Salmonella related pages select "Search Strains" from the Tasks menu i.e. Tasks -> Search Strains
).
This will open a dialogue box to set up a new search and will initially be on the "Strain Metadata" tab.
Select "City" (under heading "Location")(1) for "Field" and "London" for "Value"(2).
Then go to the "Experimental Data" tab (1 in image below), and select "Serotype Prediction (SISTR)" (2) from the Experiment Type dropdown menu. Select "Serovar" from the "Data Type" dropdown menu (3), equals from the "Operator" dropdown menu (4) and type "Typhi" in the "Value" text box (5) Press submit and a "Processing Query" box should appear.
Actually creating the tree
After a few seconds, the strains searched for should appear in the table. After the query, the number of strains will appear in the top bar (1 in image below). (This number may differ from the image below due to new strains in
the database.) Then in order to compute a SNP tree click on the tree icon (with a tree made up of straight lines)
on the top bar (2). (Mousing over the icon will display the message/ tool tip "Create SNP Project" in most modern
web browsers.) A dialog box "Call SNPs on strains" will appear. Enter a suitable name for the SNP project (making
a note of the chosen name) and
choose a reference. (For the purposes of the tutorial using the default reference is sufficient.) Then press
the "Submit" button. A dialog box "Warning: Your SNP job has been successfully submitted" should then appear. SNP
tree related pipelines will run in the order refMasker, refMapper, refMapper_matrix and matrix_phylogeny
as described in the section on SNP trees on the page about the EnteroBase backend. Depending on the size
of the job, these pipelines may take a long-ish time to run. The individual jobs running the pipelines can
be monitored by going to Tasks -> Show My Jobs
as described on this page.
Viewing the results
Once all of the SNP pipelines have finished then the results can be examined by going into
Workspace -> Load Workspace
. (Since the SNP pipelines may take a long time to run in the
case of a large job, you may have to re-visit the database search page first, in order to have
access to the menu that allows you to load the results from the completed SNP project job.) Then select
the entity with the earlier chosen name for the SNP project
and press the "load" button. Then 2 independent windows will open - a window displaying the tree
and also a JBrowse window. The window displaying the tree will also have a dialogue displayed internally
which may optionally contain a description and links. Press the "OK" button.
The page on SNP Projects describes options for displaying and manipulating the trees.
Updated