Question: Is it possible to combine gene expression data from 3' and 5' libraries?
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.
Below are some examples of performing batch correction in Seurat:
- The following tutorial shows an example using the RegressOut function:
- Alternatively, below is a tutorial for “aligning” data sets or samples which are expected to be similar (as in the case of biological replicates):