Land RemapSampleIDs.pdf

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Remap Sample IDs

This module will update the ID of a Sample (or list of Samples) in a Land. It will update both the omic data which has been loaded and the Sample Metadata but not Sample Sets.

Warning.png WARNING: To avoid conflicts, the best approach is to first Remove (not Clear) any existing Sample Metadata for the affected samples BEFORE running this module. After this module has been run and all the samples updated as needed, then re-load the correct Sample Metadata



Overview

To run this module, from the Land tab, with the relevant Land selected, click Manage | Samples | Remap Sample IDs

RemapSampleIDsMenu.png

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Input Data Requirements

Text file with two tab delimited columns mapping the existing sample ID to the new ID where the first row is assumed to be a header like:

oldID newID
Sample1 Sample101
Sample2 SampleB
Sample3 Sample4972

Note, if any of the new sample IDs already exist in the Land, the operation will fail.

This includes if the value in column 2 matches the value in column 1 to leave samples "unmapped" - this will fail!

If you need to correct a sample "swap" (e.g. SampleA's data was loaded as SampleB and vice versa), you will need to do 3 updates:

  1. Remap SampleA to SampleA.shouldBeB
  2. Remap SampleB to SampleA
  3. Remap SampleA.shouldBeB to SampleB

Warning.png WARNING: Be sure to Remove any Sample Metadata before staring the first Remap and re-load it after the final Remap (having corrected the swap in the metadata file you are loading if necessary).


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Select Land

Use the dropdown menu to select which Land to update. The default selection will be the Land that was active when you selected this menu option. All other opened Lands will be listed. If you don't see the Land you want listed, Cancel out of the dialog and open the Land using the Select Land button.

RemapSampleIDsChooseLand.png

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Browse to File

  1. Click the Browse button
  2. Navigate to & select the mapping file
  3. Click Open
  4. The File path will be populated

RemapSampleIDsBrowseToFile.png

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Send To Queue

Click Send To Queue to submit the job.

RemapSampleIDsSubmit.png

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Output Results

After the job completes, you will need to log off the Server and log back on to see the changes.


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OmicScript

RemapSampleIDs

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Related Articles

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