Thank you for developing this tool, I am very excited to try it out on my data.
I have 10xscRNAseq, and I want to get the somatic mutation in cancer cells. Initially, I did not distinguish epithelial cells as malignant and normal cells. Then, I ran the standard process as shown in the example. There are many cell types in my data, such as B cell, T cell, endothelial cell, myeloid cell. Finally, I was able to get somatic mutations that were only present in epithelial cells. Can I consider these mutations to be specific to cancer cells? Further, can the cancer cells be selected according to the mutation of each cell according to the output of SingleCellGenotype.py?
There is another problem: "To estimate new Beta binomial parameters whenever required by the user, SComatic provides the following scripts." As suggested, I have five samples, do I need to estimate new Beta binomial parameters for each sample or use the step4.1 script's default parameters?
Thank you for developing this tool, I am very excited to try it out on my data. I have 10xscRNAseq, and I want to get the somatic mutation in cancer cells. Initially, I did not distinguish epithelial cells as malignant and normal cells. Then, I ran the standard process as shown in the example. There are many cell types in my data, such as B cell, T cell, endothelial cell, myeloid cell. Finally, I was able to get somatic mutations that were only present in epithelial cells. Can I consider these mutations to be specific to cancer cells? Further, can the cancer cells be selected according to the mutation of each cell according to the output of SingleCellGenotype.py?
There is another problem: "To estimate new Beta binomial parameters whenever required by the user, SComatic provides the following scripts." As suggested, I have five samples, do I need to estimate new Beta binomial parameters for each sample or use the step4.1 script's default parameters?
Thank you in advance!
Best, Gloria