I have scRNA-seq data prepared with Smart-seq2 protocol. I have been using HISAT-StringTie-Ballgown(Partea et al. 2016) for my bulk RNAseq data.
For scRNAseq I have aligned& assembled transcripts with HISAT-StringTie. Yet, I believe normalization and further processing of transripts is different for scRNA. Any suggestions for how to process that data?