Quick search

Using the search box just above the Navigation Area on the left side of the CLC Genomics Workbench, shown in figure 3.21, you can search for

When multiple terms are entered, they are searched for individually, equivalent to putting OR between the terms. See the Advanced search expressions section below for information on creating more specific queries.

Image quicksearch1
Figure 3.21: The quick search functionality can be used to look for data elements and for information contained within metadata tables. Here, the search term "SRR1543627" has returned data elements with names or other attributes matching that term, as well as metadata tables that contain that term.

The following list of characters have special meanings when searching:

: + - && || ! ( ) ^ ] ``~* ? : \ /.

To search using these characters themselves, put quotes around the search expression. Further details are provided in Advanced search expressions section below.

Search results

If there are many hits, only the 50 first hits are shown initially. To see the next 50 hits, click on the Next (Image next) arrow just under the list of results.

The number of hits to be listed initially can be configured in the Workbench Preferences, as described in Preferences.

If no hits are found, you will be asked if you wish to search for matches that start with your search term. If you accept this, a wild card (*) will be appended to the search term.

Keeping the Alt key depressed when you click on a search result will move the focus to that data element in the Navigation Area.

Quick search history

You can access the 10 most recent searches by clicking the icon (Image recent_searches) next to the search field (see figure 3.22).

Image quicksearch4
Figure 3.22: Recent searches.

Clicking one of the recent searches runs the search again.

Advanced search expressions

Press Shift+F1 when entering a search term in the quick search box to bring up terms that can be used in search expressions, as shown in figure 3.23.

Image quicksearchguides
Figure 3.23: A list of available terms that can be used when creating advanced search expressions pops up if you press Shift+F1 after clicking in the quick search box.

Click on any entry in the list to include it in your search. For example, to search for sequences named BRCA1, select "Name search (name:)", and then type "BRCA1" to get the search expression: "name:BRCA1". The full list presented depends on the attributes available. If you have added attributes (see Customized attributes on data locations), these will also appear on the list when pressing Shift+F1.

An explanation of some available options:

Note: Wildcards cannot be used in conjunction with searches where the type of the data to search for, or in the case of metadata table contents, the columns to search within, have been specified. So, for example the search terms BRCA* and name:BRCA1 are fine, but name:BRCA* is not a valid search term.

Image find-files-boolean-terms
Figure 3.24: Elements with information that includes the term "ATP8" but not the term "mRNA" are returned using the search shown.

Searching for information in metadata tables

Searches for metadata table content can be made more specific by including a column name before the value of interest. For example, if a metadata table contains a column named "Family" containing rows with the value "Smith", you can search for Family:Smith. Forgoing the column name, i.e. searching with just the term Smith, will also find the relevant metadata tables, but will also find any other data elements that have information matching that search criteria.

The creation and use of metadata tables in CLC Genomics Workbench are described in Metadata.

Of note when including metadata table column names in searches:

To avoid running into such problems, we would generally recommend searching with just the term you wish to find, rather than specifying a column name.

Searches can be done on the contents of metadata columns of types other than Text, as described briefly below. How to specify metadata column types is described in Editing Metadata tables.

Searching using CLC URLs

A particular data element in the Navigation Area can be quickly found by entering its CLC URL into the quick search box. One example of when this can be useful is when working using a CLC Server and sharing the location of particular data elements with another user of that server.

A simple example is shown in figure 3.25.

To obtain a CLC URL for a particular data element, right click on the element name and choose the option Copy. When you then paste that information, for example in the search box or in a file or email, it is the CLC URL that is recorded.

Image quicksearch_URL
Figure 3.25: Data elements can be located using a CLC URL.