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Hi all,
I'm doing single cell RNA-seq and I'm interested in running genome-based transcriptome assembly (or de novo if necessary). The idea is that we would supplement existing GTFs in case there are significant numbers of cell type-specific alternative splice isoforms. I've been looking at various papers and algorithms (Cufflinks, StringTie, Trinity among the more recent ones), but none of them seem to be designed to work with single cell datasets. Has anybody any experience with this?
I'm doing single cell RNA-seq and I'm interested in running genome-based transcriptome assembly (or de novo if necessary). The idea is that we would supplement existing GTFs in case there are significant numbers of cell type-specific alternative splice isoforms. I've been looking at various papers and algorithms (Cufflinks, StringTie, Trinity among the more recent ones), but none of them seem to be designed to work with single cell datasets. Has anybody any experience with this?