Hi, I have a list data fields (~30) ready for extraction. I know how to extract data using the user interface, which adds one column at at time; but I wonder if there is some way to automate this process? For example, if it is possible to read in a text file that contains the data fields and output the data of these fields?
Thanks in advance.
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Are the fields all tabular data, or are they bulk fields?
For tabular data, have you discovered which instances and arrays exist for those fields?
To extract data, you could use the Table Exporter tool, see https://ukbiobank.dnanexus.com/app/table-exporter.
Alternatively, you could use the dx extract_dataset command. To use the dx commands, you first need to install dx. https://documentation.dnanexus.com/downloads#dnanexus-platform-sdk
For more information, check out the Overview video https://www.youtube.com/watch?v=uT_jD1Ey3Fk at around 18 minutes and at around 28 minutes.
@Ondrej Klempir? also wrote a tutorial on this topic here in case you prefer written guideline.
https://community.dnanexus.com/s/question/0D5t000004SBm0eCAD/query-of-the-week-1-export-phenotypic-data-to-a-file
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