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Settings
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Password
Edit

This section permits you to change your password; it is recommended that you do so on a regular basis.

Enter your old password into the "Current Password" section, and the new password into the two boxes provided for "New password " and "Confirm password". The text entered into the two boxes must match exactly or your password will not be updated.


Downloads
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This section will permit you to change how downloaded results from the RECall analysis appear when sent to your computer. The formats currently supported for downloads are: Fasta and Text. There is an option to have both formats downloaded.

Email
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It is possible to have results sent to 1 or more email-addresses when they are ready.

In order for this to be done, the checkbox must be ticked and at least one valid email address must be provided.  If more than one email address is provided, they must be separated by semi-colons, rather than commas (as you might expect).

Naming Syntax
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This is probably the most important section of the Settings panel, as it configures how sample IDs are parsed from the collection of primer sequence files. The files generated by your sequencer will vary greatly depending on which system you use, and how you have arranged your plates.

A complex example might be "E82692+2FOR_8_ES_B10_ES15.2_Run_CA_CFE3_2007-07-17_13-20_0689_078.ab1" In this case, the sample identifier is "E82692", the primer ID is "2FOR" and the rest is a collection of small ids the technologist has used to identify this particular run.

In order for all of the primer sequences from a sample to be aligned and display correctly, three elements must be parsed from the file name. The most obvious is the sample ID itself. In this case, the sample ID will be everything preceding a '+' symbol. The next will be the primer ID, and this is all of the text between the '+' and the next '_'. Everything else is assigned to the 'other' category, and is generally ignored.

You can use pull-down tabs to parse your samples, or you can write the delimiting text yourself.

This section is viewable by group SuperUsers and Administrators only.

Reference Sequences
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Reference sequences are the sequences against which other sequences are aligned and determine the scope of chromatogram that is displayed in the chromatogram view. This section is viewable by group SuperUsers and Administrators only and will permit them to add, delete and modify those reference sequences that are shared amongst your usergroup.

Check out our Uploading Reference Sequences page for more information on reference sequences.


Base Calling
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This section is viewable by group SuperUsers and Administrators only.

Mixture CutoffEdit

A nucleotide is labeled as a mixture if its largest peak is covered by another peak for at least the area set by this percentage.

The Mixture cutoff field accepts a value between 0.0 and 100.0 which represents the minimum percentage of area a secondary peak must cover before it will be considered as a mixture. The default value is 20.0%


Reducing the mixture cutoff towards 0 will increase the amount of time that the analysis requires to run.

Single CoverageEdit

Occasionally, poor quality sequencing data will cause regions of your sequence to be covered only once by good quality data. Often, it is possible to determine the sequence using only one primer sequence, however, it is best to only do this for short segments as multiple good quality primer sequences ensure accurate basecalling. The Single Coverage field allows you to set the parameters determining how much single coverage is acceptable for your analysis. The default value is zero.

Users
Edit

This section is viewable by group SuperUsers and Administrators only.

User ListEdit

This is a list of the users currently a part of your User Group. By highlighting one of the names, it is possible to review the basic properties of that particular user; what group they are a part of and their user type. It is also possible to assign a new password to that user, useful when it is lost or forgotten.

It is also possible to create a new user by highlighting the <new user> option and changing the 'Login' and 'Password' fields as appropriate.

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