CloneTracer is a methdology to add clonal resolution to scRNAseq datasets using nuclear and mitochondrial SNVs as well as CNVs. Coverage in sample-specific nuclear SNVs as well as the mitochondrial genome is increased by generating separate targeted libraries from the whole transcriptome cDNA library (Optimized 10x libraries).
For details of the method see our manuscript:
To analyse the generated data, we have developed CloneTracer, a Bayesian framework which infers the mutational hierarchy in a particular sample and probabilistically assigns single cells to clones. All required scripts and detailed explanation on how to implement the model can be found in:
In order to increase the coverage on nuclear SNVs a series of nested PCR are carried out on the whole transcriptome library. This requires mutation-specific primers. All necessary scripts to design such primers are available in:
Workflows to pre-process the mitochondrial and nuclear SNV Optimized 10x libraries can be found in:
All scripts were written by Sergi Beneyto Calabuig a member of the Velten lab at the Centre for Genomic Regulation (CRG) in Barcelona.
In case of problems or doubts about the scripts please raise an issue.