Sample Registration File

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Sample Registration File

The sample registration file contains all the information for the samples, including the sample file path and sample meta data. When registering samples, the user has the option to add Samples, Samples + SampleSets, or Samples + SampleSets + Automatic Project Creation. The automatic project creation will create a project, under a specified user’s Server Projects, that can be optionally auto-published to the server. The idea is that in many cases, there is a standard pipeline that should be run on a set of samples, and this entire pipeline should be complete before the individual user gets access to it.

Samples

Implemented using [Samples] block.

Required for any Sample Registration file.

Requirements

The first two columns have to be SampleID and FilePath.

  1. SampleID
  2. FilePath

Optional

  1. Editor: Which User Group levels will be able to change the meta data or replace the samples or SampleSets.
  2. Reader: Which User Group levels will be able to see the samples or SampleSets, and use the data.
  3. Additional columns can contain any meta data that the Lab Manager/Administrator has designated. Examples might include Time/Treatment/Group, etc. This information will be automatically appended to any design table within Array Studio. It's recommended that the user try to provide columns specified by the Sample.template file. To display information from the sample registration in the design table, simply right-click Design, and click Refresh.


SampReg3.png

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Option

Implemented using [Option] block. User can add additional options below to control the registration process:

SampleSet

The SampleSet section is optional for the Samples registration file. Please note the following:

Requirements

  1. ID: SampleSet ID is required if users want to create a sample set and run a pipeline. However, if users would like to run a pipeline without creating a sample set, a special type of SampleSet ID can be used. It is formatted as <SampleID1, SampleID2, ...>. For example ID=<GSM703914_HSB92-A1C-R, GSM703915_HSB92-AMY-R>.
  2. Additional columns can contain any meta data that the Lab Manager/Administrator has designated. It's recommended that the user try to provide fields specified by the default.template file, although additional fields are supported as well. These fields are populated to any project created by the Pipeline section.

Optional

  1. Editor line
  2. Reader line
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Pipeline

Implemented using a [Pipeline] block. Server Pipelines are server scripts created/managed by administrator. By using the [Pipeline] block, a specific pipeline (e.g. RNASeq pipeline) can be executed on the sampleset contained in this registration file, and the processed results will be included in the specified server project.

The [Pipeline] section is optional for any sample registration file.

Required Pipeline Fields

  1. One [Sample] block and one [SampleSet] block must be present in the file.
  2. UserID
  3. ScriptID
  4. AutoPublish
  5. Project.ID

Optional Pipeline Fields

  1. Parameters: If the pipeline will use non-default parameters, each parameter set must be specified as Parameter.ParameterName=NewValue
    • e.g. Parameters.ThreadNumberPerJob=2
  2. AppendMode
  3. Replace
  4. Project level meta data
  5. CC
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Example Registration Files

Sample SampleSet and Pipeline Example.txt

Sample and SampleSet only Example.txt

Sample only Example.txt

http://www.omicsoft.com/software/ArrayStudio/dbpts_sample_sampset_project.txt

If the manager or admin is uploading the file to server Instruction folder, please save the file as .osreg instead of .txt.

Workflow

SampleRegistrationWorkflow.png

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