Galaxy | Tool Preview

Cross-contamination Barcode Filter (version 0.3)

# Cross-contamination Filter Plot

For a set of barcodes and an experimental setup that uses a subset of these barcodes for each batch, this tool compares each batch against the full range of barcodes in order to determine whether any cross-contamination between batches has occured. Note -- Do not reuse batch numbering across plates!

If a significant number of transcripts are shown in a batch for cell barcodes that were not designed for that batch, then this tool will show that. In the below plot, we can see that there is no significant cross-contamination taking place (pre-filter), and so we can filter out the false barcodes (post-filter).

## Example

Consider the following experimental setup, with a list of 100 possible barcodes, used over 3 sequencing plates, with each plate containing 4 unique batches, and each plate using a specific subset of the 100 barcodes.

```Barcodes

1 - 10 | AAA AAC AAT AAG ACA AGA ATA CAC GAG TAT
11 - 20 | CCC CCA CCT CCG CTC CGC TCT GCG TCT CGT
.
.
91 -100 | TTT TAT TCT TGT TTA TTC TTG TCC TGG TAA

Plate 1  +-------+-------+-------+-------+
|  B1   |  B2   |  B3   |  B4   |
+-------+-------+-------+-------+
1-50   51-100  51-100   1-50

Plate 2  +-------+-------+-------+-------+
|  B5   |  B6   |  B7   |  B8   |
+-------+-------+-------+-------+
1-40   41-80    1-40   41-80

Plate 3  +-------+-------+-------+-------+
|  B9   |  B10  |  B11  |  B12  |
+-------+-------+-------+-------+
1-40   41-80    1-40   41-80
```

The above plate and barcoding setup can be more textually represented by specifying barcode ranges and plate numbers, with each denoting which batch numbers they describe as outlined below:

```*Barcodes → Batches*
1- 50: B1, B4
51-100: B2, B3
1- 40: B5, B7, B9 , B11
41- 80: B6, B8, B10, B12

*Plates → Batches*
1: B1, B2 , B3 , B4
2: B5, B6 , B7 , B8
3: B9, B10, B11, B12
```