Entering edit mode
9 months ago
wangjb702
•
0
Hi everyone,
Recently, I got my snRNA-seq data. But after aligned to reference genome using cellranger, I got a wired barcode rank plot. what should I do next to correct this data?
Thanks in advance
The knee plot is just one type of QC. I'd say just proceed with your analysis and see if you observe anything funky (analysis itself is a QC). You should also see if you can use a tool that removes doublets and ambient RNA, if that helps your analysis.
Agreed. I would just force the cells to 5000 or so, and then proceed with the normal QC. If there's a lot of trash "cells" in the dataset this will manifest by poor QC metrics such as number of detected genes and mitochondrial expression percentage (since mt genes usually are highly-expressed so they're always detected first), plus "trash" tends (in my experience) to cluster together with marker genes that make no biological sense. Just try a bit, see what works.