Can I combine gene expression data from 3' and 5' assay chemistries?

Question: Is it possible to combine gene expression data from 3' and 5' libraries?

Answer: The cellranger aggr pipeline can combine 3' and 5' gene expression data. However, cellranger aggrdoes not correct for chemistry-specific effects. 

Normalization and correcting for systematic or batch effects in single cell RNA seq data are areas of active research, and at present, we don't offer specific recommendations. 

There are a number of packages in R that address batch correction issues (e.g., Seurat(1), scran(2), and scone).

Here are some resources for performing batch correction in Seurat:

1. A tutorial on using the RegressOut function:
   • https://github.com/broadinstitute/single_cell_analysis/blob/master/cegs_2017_demo.md#seurat-batch-effect-correction
2. A tutorial on aligning datasets or samples that are expected to be similar (as in the case of biological replicates):
   • http://satijalab.org/seurat/Seurat_AlignmentTutorial.html

References:

(1) Butler, Andrew, and Rahul Satija. "Integrating single-cell transcriptomic data across different conditions, technologies, and species." Nature Biotech (2018).

(2) Haghverdi, Laleh, et al. "Batch effects in single-cell Rna-sequencing data are corrected by matching mutual nearest neighbors." Nature Biotech (2018).