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:
- 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):
References: