What to do if demultiplexing is not done correctly or the results are not as expected?

If the wrong barcodes were selected, use one of the two options:

1. SMRT Link: use the Data Utility “Undo Demultiplexing” (make sure to run on the parent dataset) and then redo demultiplexing with the correct barcode file using the Data Utility “Demultiplex Barcodes”
2. Command line: use lima-undo to undo demultiplexing followed by lima for demultiplexing with the correct barcode fasta file

If barcodes are missing or scores look low and you want to investigate what barcodes might be in the sample that were missed, try using the command line tool lima with –peek-guess