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: Although cellranger aggr command will successfully combine 3' and 5' gene expression data. However, even though Cell Ranger will successfully generate a matrix, it will not correct for chemistry-specific effects. 

In general, 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 have a specific recommendation. 

From the literature, there are a number of packages in R, such as Seurat (1), scran (2), and scone, which attempt to address these issues.

Below are some examples of performing batch correction in Seurat:

1. The following tutorial shows an example using the RegressOut function:
   • https://github.com/broadinstitute/single_cell_analysis/blob/master/cegs_2017_demo.md#seurat-batch-effect-correction
2. Alternatively, below is a tutorial for “aligning” data sets or samples which 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).