I am working on a single cell rnaseq dataset for two conditions. 10X genomics protocol and Novaseq platform was used to sequenced the single cells. BCL to FASTQ has been performed. Then I ran cellranger count pipeline on those FASTQ files to get the output files.
As per the summary, - Condition A has been estimated to have 1500 cells (28,000 mean reads per cell, 2,000 median genes per cell) - Condition B has been esitmated to have 500 cells (10,000 mean reads per cell, 600 median genes per cell)
1) How to find percentage of a gene (eg.Ppbp) for condition A in 1500 cells?
2) How to find percentage of a gene (eg. Ppbp) for condition B in 500 cells?
For both questions 1 and 2, This is what I am planning to do, count the number of cells which expresses this gene Ppbp. Which output file from cellranger count pipeline should be used to get the cells and genes count matrix?
How to do cell subpopulations for the filter gene?