Best Pipeline for De novo transcriptome SC-RNAseq
I’m curious what the best pipeline for single cell RNA seq is if your organism of interest doesn’t have a genome. Tools such as CellRanger need a reference genome, and bustools seems to need a reference for indexing.
Is the best approach to trim the UMIs from the files and perform a de novo assembly using a tool like trinity, then use this as the reference genome for CellRanger / Bustools?
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