How to Specify Barcodes

This article describes how to specify and name barcode sequences when using the Collapse UMI duplicates and Separate Barcodes pipeline. If you are unsure what barcodes are used for, please see this article to learn about Single Clone/Cell technologies.

Entering Barcodes

Specify each barcode on a separate line. Each barcode must contain a barcode name followed by the barcode sequence, separated by a space or tab. If no space or tab is entered, the barcode name will be assumed to be the same as the barcode sequence.

Examples:
Spleen GATTACA
Thymus CCGGACA

If barcodes are direction-specific and the sequences are randomly orientated, barcodes should be classified as forward to reverse so that forward and reverse sequences can be grouped together in the results.

Example:
Forward:
Barcode-1-F GATTACA
Barcode-2-F CCGGACA
Reverse:
Barcode-1-R TTTTTTT
Barcode-2-R GGGGGGG

If there are multiple barcodes on each end of the sequence, barcodes should be classified according to their position relative to the edge of the sequence using a section prefix of 1: for the first barcode and 2: for the barcode that appears immediately downstream of the first barcode.

For example, the following syntax specifies a plate then row barcode on the 5' and plate then column on the 3' end of each sequence.

1:
Forward:
Plate1-F GATTACA
Plate2-F CCGGACA
Reverse:
Plate1-R TTTTTTT
Plate2-R GGGGGGG

2:
Forward:
Row-1 CCCCC
Row-2 TTTTT
Reverse:
Column-A GGGGG
Column-B AAAAA