Minor changes to Generating PCR plate

Minor changes to Generating PCR plate including correcting spelling,
quotations, dropdown menu options. Also,
- Added in link for naming conventions
- Added a note about the inability to modify cocktails

Docs/pcr_plates.rst

@@ -35,13 +35,13 @@ From this point forward, generating new plates, whether PCR or cycle sequencing,
   :align: center 
 
 * If the reaction types are the same (for example, creating an extraction plate as a working aliquot from an archival extraction plate), then all reaction parameters will be copied to the new plate. If the reaction type is different (for example, creating a PCR plate from an existing extraction plate), then only the extraction ID's will be copied across.
-* Select the Type of reaction as PCR, click OK and a ‘New PCR' plate window will appear.
+* Select the Type of reaction as PCR, click OK and a "New PCR" plate window will appear.
 
 .. figure:: /images/empty_pcr_plate.png
   :align: center 
 
-* Enter a plate name in the box provided. This name should be descriptive and unique to allow easy and successful searching in the LIMS. 
-* The next step is to select the thermocycling protocol that was used for this PCR plate. The Geneious LIMS stores thermocycling profiles and these are found in the ‘Example Thermocycling' dropdown menu in the New PCR plate Toolbar. Creating new profiles is described in the Additional Information section at the end of this document.
+* Enter a plate name in the box provided. This name should be descriptive and unique to allow easy and successful searching in the LIMS. The BWP naming conventions protocol is found here: http://bwp-informatics.readthedocs.io/en/latest/conventions.html
+* The next step is to select the thermocycling protocol that was used for this PCR plate. The Geneious LIMS stores thermocycling profiles and these are found in the "Example Thermocycling" dropdown menu in the New PCR plate Toolbar. Creating new profiles is described in the Additional Information section at the end of this document.
 * Next, to edit all wells on the PCR plate, select "Edit All Wells". Alternatively, to edit individual wells, highlight the selected wells in the plate and click "Edit Selected Wells" in the plate toolbar. In both cases the "Edit Wells" window opens. 
 
 .. figure:: /images/edit_pcr_wells.png
@@ -53,7 +53,7 @@ From this point forward, generating new plates, whether PCR or cycle sequencing,
 * A PCR reaction can be marked as "not run", "run", "passed" or "failed". 
 * The forward and reverse PCR primers are selected using the "Choose" button which points to a selected folder on the local directory where primers are stored by the user.
 * The reaction cocktail can be chosen from a list of existing cocktails, or by creating a new cocktail, described in the Additional Information section at the end of this document.
-* Gel images can be uploaded by clicking the "Gel Images' button in the plate window and pointing to the relevant file. More information on attaching a gel image and scoring is available in the Additional Information section below.
+* Gel images can be uploaded by clicking the "Gel Images" button in the plate window and pointing to the relevant file. More information on attaching a gel image and scoring is available in the Additional Information section below.
 * Once all editing of the plate is complete, Click OK. 
 
 Additional Information
@@ -84,7 +84,10 @@ Creating custom PCR cocktails:
 
 * Click "Edit Cocktails", then click the + button in the dialog, and enter the volumes and concentrations in the fields provided. 
 * There is space to store one extra ingredient (both concentration and volume) that isn't in the provided ingredient list. 
-* Any additional information about the new cocktail can be stored in the Notes field. It is not possible to modify cocktails once they are created and cocktails can only be deleted if they are not associated with a workflow.
+* Any additional information about the new cocktail can be stored in the Notes field. 
+
+.. note::
+It is not possible to modify cocktails once they are created, and cocktails can only be deleted if they are not associated with a workflow. Cocktails are available also to all users. As a result, double check that the cocktail you require doesn't already exist prior to creating it.
 
 .. figure:: /images/edit_cocktails.png
   :align: center 
@@ -99,7 +102,7 @@ Once the image or images are attached, click the "Split GEL" button located abov
 .. figure:: /images/score_pcr.png
   :align: center 
 
-To verify the scoring of the gel image, re-open the plate view. It is possible to manually change the call by selecting the well in the plate viewer and changing the scoring in the drop-down menu.
+To verify the scoring of the gel image, re-open the plate view. It is possible to manually change the call by selecting the well in the plate viewer and changing the reaction state in the drop-down menu. The program may score primer dimers in the gel, so if they are present, extra care should be taken and the calls double checked. 
 
 .. figure:: /images/pcr_plate_with_gels.png
   :align: center