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Custom Barcodes being rejected by Guppy barcoder due to File Encoding type. How do I resolve this?

It has been observed that the following error can occur when trying to utilize Guppy for demultiplexing custom barcodes:

"Barcode 'CUST001_FWD' was referenced in arrangement, but not found in barcode file."

If this error occurs, please ensure that the Guppy user manual has been closely followed and that all the appropriate files are being utilized and are correctly formatted. Verify that the barcode reference file does contain the correct barcode names and sequences.

If all the required files have been made correctly and verified but the above error still occurs, check the type of file encoding of each input file. In rare cases this error can be caused due to an altered file encoding.


Using a text editor like Sublime, change the file encoding to UTF-8.

Sublime does not show encoding in its default state. To add this feature open Sublime and navigate to:

Preferences > Settings

Add the following code in-between the curly brackets in the settings panel on the right:

"show_encoding": true,

"show_line_endings": true

This will now show file endings and encodings in the grey row at the bottom right of the Sublime window. Clicking on the encoding type (“UTF-16 LE with BOM”) will open a list of encodings. Set this to UTF-8.

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