Issue with Pairing KB-6392 reopened
Advantages
For new projects, a sample table can be automatically created from a tab-delimited text file. There are several advantages of creating a sample table in this manner:
- You can define multiple samples and attributes even before data has been imported, and therefore you can:
- customize the name of your samples (and not use the automatic sample names generated based on file names)
- import sample sheets as defined by the instrument that generated your data
- You can simultaneously create the sample table and import data, which allows you to:
- combine several files into one sample
- import data located in multiple subdirectories
Creating and Selecting the Text File
The text file must be created outside of Partek® Flow® (using other software such as Partek® Genomics Suite®, Microsoft® Excel® or any other text editor). A valid text file is a tab-delimited text file that contains at least one column that has unique entries (to be used as Sample IDs) and may have additional columns with sample information such as experimental attributes and (optional) filenames.
In a Data Tab where no samples have been imported yet (Figure 1), click the Assign sample attributes from a file button.
Figure 1. A New project with no samples in the Data Tab
Navigate to the file using the browser as shown in in Figure 2. Check the box next to the text file that you want to use and click Next.
Figure 2. Locating a text file that contains sample information
Depending on the content and location of the text file, creating the sample table can be done with or without data import.
Creating a Sample Table without Data Import
Text files that contain only sample information and attributes such as the one shown in Figure 3 can be imported to create a sample table with no associated files. For this type of import, the text file may be located in either the Partek Flow server, My computer, or from a URL (Figure 2).
Figure 1. Text with Attributes
The text file will be summarized as in Figure 4. The first two columns show the headers and example terms from the text file (Figure 3). The suggested Attribute names can be edited before import. Columns that contain unique entries are recognized as possible Sample IDs and you can select using the radio button in the fifth column. You can also choose which attributes to be included and (if applicable), whether they are numeric or categorical. The Show/hide file preview link allows you to preview the text of the tab delimited text file you are using.
In the example in Figure 3, the columns for "Sample name" and "Freezer Location" are both unique and the former is selected as the Sample ID. The "Freezer location" has been deselected and it will not be included in the Sample table. Since "Age" has number terms, the Attribute type column is a drop down menu to choose between Numeric and Categorical. There are no filenames in the text file so the Files column is empty.
Figure 3. Selecting the attributes and Sample ID
Click import and the table will be created (Figure 5). Each row is a sample in the project. However, there are no but is not associate with any file. Click Show data files to expand the table and associate files. For more details see the relevant section here.
Creating a Sample Table with Data Import
Currently, filenames should be separated by tabs (if in a table, each file should be in a different column... maximum one file per column)
A feature of creating the sample ability to combine this step with data import ... the additional feature of importing samples during table creation (described below) are currently only available if the text file is in the Partek Flow Server.
can only be at the same time as creating the sample table) can only be performed if
a sample table that also includes the locations of filenames can only be based on the sample table (as described later in this section)
The text file must be in the server or a folder that is readable by the partek flow server. the text file contains filenames
A valid text file:
TABLE TEXT FILE NO PATH
useful if there are many files for one sample, You can add as many columns as you want on the right
Flow recognizes sees that some columns in your text file are filenames of
FIGURE OF NAVIGATION... SHOW THAT THE DATA IS IN THE SAME DIRECTORY MYDATA
FIGURE WITH FILENAMES
FIGURE RESULTING TABLE
FIGURE IMPORT task
FIGURE EXPANDED TABLE
In the example above, the text file and Data files are in the same directory. If your samples are in different subdirectories, YOU CAN USE PATHS. RELATIVE OR ABSOLUTE
Relative path
FIGURE NAVIGATION... SHOW THAT THE DATA IS DIFFERENT DIRECTORY THAN MY DATA
TABLE RELATIVE PATH
Relative to the text file
Absolute path
FIGURE NAVIGATION SHOW THAT THE DATA IS IN DIFFERENT DIRECTORY AND the directory structure starts with /home/directory....
TABLE ABSOLUTE PATH
you must write the path this way
For a short video of using a text file, please see. the
Note that this can only be done on a blank project... once you have any import
Additional Assistance
If you need additional assistance, please visit our support page to submit a help ticket or find phone numbers for regional support.
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