Hi all! I have single cell RNA sequencing data that I have filtered, normalized, etc. I now want to know how many transcripts I have from a specific gene in my data and I want to see this data represented in a few different ways. For clarity's sake, the gene I'm interested in is PIK3CA.
I want to figure out a way to a) count the amount of PIK3CA transcripts there are in my data set b) count the amount of PIK3CA transcripts that are in specific clusters (let's pretend it's clusters 1 and 2) c) know the range of how many PIK3CA transcripts are present per cell from my total data d) know the average number of PIK3CA transcripts are per cell from my total data e) know the range and average of number of PIK3CA transcripts per cell for clusters 1 and 2
So far I have made a subset of my data that only contains PIK3CA positive cells with an average expression of 0.21 or higher (my average expression range for PIK3CA in my data is 0.21-4). But I'm starting to feel like that is unnecessary because it does not solve the problem of filtering for the number of PIK3CA transcripts. As far as I can tell that information is buried within nCount_RNA (number of UMIs detected in each cell). But I learned coding basics back in March and I'm super rusty with how to manipulate these factors to filter for my gene of interest or further parse this info for my individual clusters.
Thank you in advance!