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bcgsc / NanoSim

Nanopore sequence read simulator
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Can NanoSim be applied to simulate single cell Nanopore reads #180

Open yuntianf opened 1 year ago

yuntianf commented 1 year ago

Hi, Thanks for the great tool. As the title, I'm wondering if this tool can be applied to simulate single cell Nanopore reads. I'm thinking to generate bunch of transcripts for a gene and attach them with cell barcodes and UMIs. Then use a simulator to introduce sequencing errors and truncations in. I went over the document for NanoSim, the transcriptome mode just simulated reads according to transcritome fasta and TMP as quantification, which seems just for bulk sequencing. I'm wondering if there is any way that this tool could be used to generate single cell Nanopore sequencing!

kmnip commented 1 year ago

The main obstacle is to model the transcriptome heterogeneity within a population of cells. At the very least, there needs to be a model for the transcript expression profile for each cell in a given population. So, it wouldn't work out of the box in my opinion.