How to analyze mars-seq single end-read scRNAseq data?
1 answer
CellRanger is specific to the 10x Chromium technologies. You cannot use it here. Do you really need to process the data from scratch? This dataset (Paul et al) is included in the Bioconductor package scRNAseq. You can download the count tables via scRNAseq::PaulHSCData(). I used this dataset via this package for my own work before, it is fine.
See for more info: https://bioconductor.org/packages/release/data/experiment/vignettes/scRNAseq/inst/doc/scRNAseq.html
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