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