Genotyping
----------

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Defining Locus types and attributes
***********************************

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   A Locus type is a category of locus or genetic markers with common descriptors. It is one of the descriptors of an :ref:`Locus<Locus management>`. For instance, a locus type can be SNP, SSR, RFLP etc.

   Locus type can be managed in the menu *Admin > Genotyping > Locus type*.

   It is defined by the fields described in the table below. Fields in bold are required while italic ones are optional when submitting the :ref:`form<Form>`.
   

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   .. figure:: /_img/admin/LocusMenu.png
   
      *Locus administration menu*

Locus types can be edited from the :ref:`table<Table>` below the form.

+---------------+---------------------------------------------+
| Field name    | Description                                 |
|               |                                             |
+===============+=============================================+
|               | The name of this locus type                 |
| **Name**      | (for instance : SNP, SSR, Genomic sequence) |
+---------------+---------------------------------------------+
|               | A text describing this locus type           |
| *Description* |                                             |
+---------------+---------------------------------------------+

:ref:`Locus<Locus management>` are described regarding a set of fixed attributes (see below), common to all locus types. Thaliadb makes possible to add specific attributes to each locus type.   
Attributes can be managed in the menu 'Attributes' in the left navigation toolbar. An attribute is defined by the fields described in the table below. Fields in bold are required while italic ones are optional when submitting the :ref:`form<Form>`. Attributes can be edited from the :ref:`table<Table>` below the form.
   

+---------------+-------------------------------------------------------------------------+
| Field name    | Description                                                             |
|               |                                                                         |
+===============+=========================================================================+
|               | The name of this attribute                                              |
| **Name**      |                                                                         |
+---------------+-------------------------------------------------------------------------+
|               | A type defining the nature of the information to choose between :       |
| **Type**      | Short text, Long text, Number, URL                                      |
|               | The type will have consequences on the look of the widget in Locus form |
+---------------+-------------------------------------------------------------------------+
|               | A short description for this attribute                                  |
| *Description* |                                                                         |
+---------------+-------------------------------------------------------------------------+

As soon as your attributes are defined you can add them as additional descriptors in locus type. Adding attributes to a locus type will enrich the fields available when you create a new locus of this type. To do so, go back to the Locus type table and edit one of them. A new tab 'Attributes' will appear in the edition form.

In this interface, you can add attributes to the current locus type (1). By default, this attribute will be added at the last position. You can change this order by drag'n drop, as soon as you're fine with your attributes order you can click on the 'Save order' button (2).
This order that you defined will be respected in the Locus form and when you will export locus data from thaliadb.

.. figure:: /_img/admin/Attributes-management.png
   :align: center
   
   *Locus type attributes management works as Accession type attributes management*

Locus positions
***************

Locus management
****************

A Locus is a fixed position on a chromosome. This :ref:`position<Locus positions>` can be known or not and can be different from a :ref:`genome version<Genome versions>` to another.

Locus can be managed in the menu *Admin > Genotyping > Locus type*. In the left navigation toolbar, a menu is available for each :ref:`locus type<Defining Locus types and attributes>` that have been defined in the tool.

It is defined at least by the fields described in the table below (additional fields can be defined as explained in the previous section). Fields in bold are required while italic ones are optional when submitting the :ref:`form<Form>`. Locus can be edited from the :ref:`table<Table>` below the form.


+------------------+-----------------------------------------------------------------------------------+
| Field name       | Description                                                                       |
|                  |                                                                                   |
+==================+===================================================================================+
|                  | The name of this Locus                                                            |
| **Name**         |                                                                                   |
+------------------+-----------------------------------------------------------------------------------+
|                  | A description for this Locus                                                      |
| *Comments*       |                                                                                   |
+------------------+-----------------------------------------------------------------------------------+
|                  | If position is known for this locus, the genome version on which it is positioned |
| *Genome version* |                                                                                   |
+------------------+-----------------------------------------------------------------------------------+
|                  | If position is known for this locus, the chromosome on which it is positioned     |
| *Chromosome*     |                                                                                   |
|                  |                                                                                   |
+------------------+-----------------------------------------------------------------------------------+
|                  | The position of this locus if it is known                                         |
| *Position*       |                                                                                   |
|                  |                                                                                   |
+------------------+-----------------------------------------------------------------------------------+


Referential
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Experiment
**********

Genome versions
***************

Sample
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GenotypingID
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Insert Genotyping data
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