Search Genotypic Datasets

• Search for Genotypic Data by Dataset
  • Before you begin
  • Open the Genetic Dataset Search window
  • Choose one or more genetic datasets
  • Optional: choose one or more genetic maps
  • Continue to genotypic dataset options
  • Select output options
  • Run the query
  • Recommended workflows
    • Retrieve all records for a specific genotypic dataset
    • Retrieve summarized cultivar/line genotypic data
    • Search using a genetic map only
  • Troubleshooting
  • Quick reference

Search for Genotypic Data by Dataset

Use this tutorial when you want to retrieve genotypic records from datasets already loaded in CIERA. The search starts from the Data Search > Genotypic Data > Search for Genotypic Data by Dataset menu choice.

Before you begin

• Open CIERA and sign in to the database you want to search.
• Confirm that the genotypic dataset or genetic map you need has already been loaded.
• If you plan to export or analyze the results, know whether you need only the line/GID-level genotypic records or the entire marker dataset.

Open the Genetic Dataset Search window

CIERA - Search for genotypic data by datasets

1. From the CIERA main window, open Data Search.
2. Point to Genotypic Data.
3. Select Search for Genotypic Data by Dataset.
4. The Genetic Dataset Search window opens.

Choose one or more genetic datasets

1. In the first tree list, labeled Please select a genetic dataset from the following list:, expand folders until you can see the dataset names.
2. Check the box next to each genetic dataset you want to include.
3. To include every available genetic dataset, check Click to choose all genetic datasets.
4. Do not select folders only. CIERA uses checked dataset records for the search; folder names are for organization.

Optional: choose one or more genetic maps

1. In the second tree list, labeled If you wish, please select a genetic map from the following list (optional), expand the map folders.
2. Check the box next to each genetic map you want to include.
3. To include every available genetic map, check Click to choose all genetic maps.
4. You can continue without choosing a genetic map if your search only needs dataset records.

Continue to genotypic dataset options

1. After selecting at least one dataset or map, click Next.
2. If CIERA warns that you must choose at least one dataset or map, return to the tree lists and check at least one dataset or map item.
3. The Genotypic Dataset Options window opens.

Select output options

On the Genotypic Dataset Options window, choose the options that match your retrieval goal.

• Summarize genotypic cultivar data: Check this when you want CIERA to summarize genotypic data by cultivar/line. Use this option carefully for very large marker sets; the screen warns that summarizing hundreds of markers or more may take an hour or longer.
• Show entire dataset(s): Check this when you need the full selected dataset output instead of only the default GID-level data.

If you selected only a genetic map and no genetic dataset, CIERA disables the dataset-specific options and notes that no dataset options are available.

Run the query

1. Click Next on the Genotypic Dataset Options window.
2. CIERA runs the genetic dataset query for the selected datasets and/or maps.
3. Review the output window when results appear.
4. If the query takes longer than expected, wait for processing to finish, especially when summarization or large marker datasets are selected.

Recommended workflows

Retrieve all records for a specific genotypic dataset

1. Open Data Search > Genotypic Data > Search for Genotypic Data by Dataset.
2. Check the dataset name in the genetic dataset tree.
3. Leave the genetic map tree unchecked unless a map is needed.
4. Click Next.
5. Check Show entire dataset(s).
6. Click Next to run the query.

Retrieve summarized cultivar/line genotypic data

1. Open Data Search > Genotypic Data > Search for Genotypic Data by Dataset.
2. Check one or more dataset names.
3. Click Next.
4. Check Summarize genotypic cultivar data.
5. Leave Show entire dataset(s) unchecked unless you also need the complete dataset output.
6. Click Next to run the query.

Search using a genetic map only

1. Open Data Search > Genotypic Data > Search for Genotypic Data by Dataset.
2. Leave the genetic dataset tree unchecked.
3. Check one or more maps in the genetic map tree.
4. Click Next.
5. Confirm that the options screen says only a genetic map was chosen.
6. Click Next to run the query.

Troubleshooting

• No datasets or maps are listed: Confirm that genotypic datasets or maps have been loaded into the connected database.
• The Next button shows a warning: Select at least one dataset or map before continuing.
• The output is larger than expected: Return to the search and leave Show entire dataset(s) unchecked if you only need default GID-level data.
• The query is slow: Summarization and full-dataset output can be slow for datasets with hundreds or thousands of markers.
• You closed a search window by mistake: CIERA asks whether you want to quit the search. Choose No to return to the search window or Yes to cancel.

Quick reference

Goal	Dataset selection	Map selection	Option selection
Get full genotypic dataset output	Select one or more datasets	Optional	Check Show entire dataset(s)
Get default dataset records	Select one or more datasets	Optional	Leave Show entire dataset(s) unchecked
Summarize by cultivar/line	Select one or more datasets	Optional	Check Summarize genotypic cultivar data
Search by map only	Leave datasets unchecked	Select one or more maps	No dataset options available