Hi!
Thank you for sharing such an amazing resource! I have a question regarding your metadata file called "table_S2.xlsx". The $QC column contains 4 values: NA, doublets, "Doublets?", and "bad cells".
Here is what I know about them:
a) As far as I can tell, these are valid cells (as defined by your h5 object).
b) They also do not come from samples that did not pass QC as indicated in "table_S1.xlsx".
c) These cells are also not doublets as they do not pass the threshold for doubletflag.
When I visualize their quality control metrics, bad cells do not stand out (NA Cells are all other cells).
I checked the "Science" manuscript and I couldn't find a mention of this quality control step in the methods section.
My question: Should I remove these cells as another layer of quality control?
Hi!
Thank you for sharing such an amazing resource! I have a question regarding your metadata file called "table_S2.xlsx". The $QC column contains 4 values: NA, doublets, "Doublets?", and "bad cells".
Here is what I know about them:
a) As far as I can tell, these are valid cells (as defined by your h5 object).
b) They also do not come from samples that did not pass QC as indicated in "table_S1.xlsx".
c) These cells are also not doublets as they do not pass the threshold for doubletflag.
When I visualize their quality control metrics, bad cells do not stand out (NA Cells are all other cells).
I checked the "Science" manuscript and I couldn't find a mention of this quality control step in the methods section.
My question: Should I remove these cells as another layer of quality control?