Question: Can I aggregate gene expression data from different chemistries? For which ones should I use chemistry batch correction?
Answer: cellranger aggr pipeline can be used to combine data of two or more libraries. For combining data from the same chemistry, default options of cellranger aggr pipeline can be used. However, if you are combining data from different chemistries, you may need to use chemistry batch effect correction. The following table shows various chemistry combinations with their compatibility in the cellranger aggr pipeline and our recommendations.
|
Assay Chemistry |
3’ v1 |
3’ v2 |
3’ v3 |
3’ v3.1 |
3'v4 |
5’ v1 |
5’ v1.1 |
5' v2 |
5' v3 |
|
3’ v1 |
Supported. Do not use chemistry correction. |
Possible * |
Possible * |
Possible * |
Possible * |
Not supported |
Not supported |
Not supported |
Not supported |
|
3’ v2 |
|
Supported. Do not use chemistry correction. |
Supported. Use chemistry correction. |
Supported. Use chemistry correction. |
Possible * |
Possible * |
Possible * |
Possible * |
Possible * |
|
3’ v3 |
|
|
Supported. Do not use chemistry correction. |
Supported. Optional to use chemistry correction. |
Possible * |
Possible * |
Possible * |
Possible * |
Possible * |
|
3’ v3.1 |
Supported. Do not use chemistry correction. |
Supported. Use chemistry correction. |
Possible * |
Possible * |
Possible *
|
Possible * |
|||
|
3' v4 |
Supported. Use chemistry correction. |
Supported. Do not use chemistry correction. |
Possible * |
Possible * |
Possible *
|
Possible * |
|||
|
5’ v1 |
|
|
|
|
Supported. Do not use chemistry correction. |
Supported. Optional to use chemistry correction. |
Supported. Use chemistry correction. |
Possible * |
|
|
5’ v1.1 |
Supported. Do not use chemistry correction. |
Supported. Use chemistry correction. |
Possible * |
||||||
|
5' v2 |
|
Supported.
Do not use chemistry correction. |
Supported. Use chemistry correction. |
||||||
|
5' v3 |
|
Supported. Use chemistry correction. |
Supported. Do not use chemistry correction. |
Possible *: indicates that cellranger aggr pipeline will process the data with chemistry correction. However, it is not a validated intended usage. Results will likely vary and should be interpreted with caution. Additional technical or batch effects may remain.
The chemistry batch correction algorithm has been validated for combining 3’ v2 with 3’ v3, 3'v3.1 with 3'v4, 5' v1 with 5' v2 and 5' v2 with 5' v3 chemistry datasets. Using the correction for combining data from other chemistries could improve the mixing of the batches. However, we advise careful validation of the results. In the above table, the phrase "Supported" indicates that we have validated batch correction on merging this combination and have data to support it.
When aggregating 3' v3 and 3' v3.1 data, it is not necessary to use chemistry batch correction. However, if you think it might be helpful for your analysis, we encourage the usage of chemistry batch correction in this case.
Note that data analyzed using Cell Ranger versions prior to 1.2 are not compatible with cellranger aggr pipeline.
Related Articles:
- Can I use aggr to combine 3’ LT v3.1 data with standard 3’ v3.1 data? Will there be chemistry batch effects?
- Can I use Cell Ranger aggr to combine data from HT kits with data from standard kits? Will there be chemistry batch effects?
Products: Single Cell Gene Expression
Last Updated: March 13, 2024