I am currently analyzing single-cell data gathered using the iCell8 platform (Takara) that captures full transcripts using the SMART-seq v2 chemistry. The official pipeline by Takara (CogentAP) uses STAR for alignment and so far offers no convenient possibility to investigate the transcript-specific data that is present in the full-length data generated by SMART seq v2.
However, I am mainly using Seurat for analysis anyway and really like the convenience of having all the tools in a clean and consistent package. I have searched for a few hours but so far couldn't find out if there is a good possibility to leverage the transcript information and use it in or in combination with Seurat. Does anyone know if and how this can be achieved?
STAR at least generates some data on exon usage that is stored in the analysis output of CogentAP but not used further. Could this be used for analysis in another tool and then integrated into Seurat using the cell barcodes to enhance the existing analysis based on gene count data? Could I even generate some sort of transcript expression matrix using kallisto or salmon and load that into Seurat instead of a gene expression matrix in the first place?
Thanks a lot for any input!