I am trying to analyze data for a single cell RNA sequencing experiment, for QC and normalization I am considering using the scater package. There are a few things I would like to know before starting analyzing this dataset. All your help and suggestions are much appreciated. This is my first attempt to analyze sc-RNA, I apologize in advance if my questions are confusing. Questions: 1) The sequencing lab is using an unpublished protocol, they have provided read counts and spike-ins file separately. Do I need to combine these two files? I am considering this, for the "feature_controls" option for calculateQCMetrics method.
2) After doing the initial QC, I see that total counts for all my wells(cells) is almost >50k+ and the number of genes detected is above 10k. I am removing genes that have 0 expression, I am also filtering genes with very low average nonzero expression across all cells(using a mean of counts across all cells). Do I need to do any other filtering for both cells and genes?
Also, I would greatly appreciate, if you could direct me to a sample reference analysis.