thek71
commented
5 days ago Hi Krithika,
epiAneufinder processes each cell independently from all other cells in the dataset. Since there is no shared information and you get one CNV profile per cell, if you filter your cells before the CNV calling or after it makes no difference. The only thing to consider here is the run time, since the more cells you have the more time you will need for calling CNVs for all.
Best, Katia
Hello authors,
Sorry to trouble you, more questions related to fragment file. So I used the fragments file and was able to get EpiAneufinder running on my dataset which is a sn-multi-ome dataset.
I have a WNN seurat object after running sn-multi-ome pipeline on the snRNA-seq and snATAC-seq. At this point I have about 134,000 cells in the WNN object.
When I ran EpiAneufinder, it ran on the fragment files which contained all the cells, and now I have sub-clone annotation on about 300,000 cells.
Question 1) Should i filter the fragment file first to include only the cells from the WNN object to begin with, and run epiAneufinder on those 134,000 cells ? OR 2) Start with the full set of fragment files and run Epianeufinder. Then Extract the CNV and sub-clonal annotation of the 134,000 cells , and add to the WNN metadata
Unsure which is a better way to proceed, and would love your feedback.