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jon-xu / scSplit

Genotype-free demultiplexing of pooled single-cell RNA-Seq, using a hidden state model for identifying genetically distinct samples within a mixed population.
MIT License
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Question: Bulk nanopore RNA-seq? #18

Closed alexandruioanvoda closed 2 years ago

alexandruioanvoda commented 2 years ago

Hi! Really cool method!

I was wondering whether your package would support bulk RNA-seq? And nanopore-based (i.e. not Illumina short) reads? Is support for other genomes (e.g. other mammalians) easily configurable?

jon-xu commented 2 years ago

Thanks for the interest! Unfortunately this tool is designed for single cell RNA-seq, and thus cannot support bulk data. As to nanopore, if it is single cell, once you have mapped the long reads and called variants using nanopore tools, the rest should be the same, but we haven't tested it. The support for other genomes is easy because we only need the BAM file and don't care which genome it used for mapping.