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robertaboukhalil / ginkgo

Cloud-based single-cell copy-number variation analysis tool
qb.cshl.edu/ginkgo
BSD 2-Clause "Simplified" License
47 stars 28 forks source link

Can Gingko be used to determine CNVs from single cell RNA seq data? #10

Closed kragrawa closed 6 years ago

kragrawa commented 6 years ago

Hi I wanted to know if Gingko could be used to determine CNVs from single cell RNA seq data, or does the data have to be DOP-PCR and MALBAC data? Thank you!

mschatz commented 6 years ago

Ginkgo is only designed for DNA analysis. There have been a few approaches to predict CNVs from RNAseq, but requires a totally different framework to account for the variable expression of genes across different cell types. Good luck! Mike