Question: Seurat Integration Post-Normalization and Cluster Identification or Pre those Steps
0
gravatar for fouerghi20
4 months ago by
fouerghi2030
fouerghi2030 wrote:

I have two samples that I have analyzed separately using the Seurat pipeline, which means I currently have two Seurat objects that I have run the normalization on. I am currently thinking about integrating the two samples, so I can run the analysis on it. In my current workflow, I integrate the two samples after having run the normalization, scaling and assigned cell types by identifying the clusters through the marker genes. I am wondering if it is a better practice if I integrate the two samples, and then normalize them, find the variable features, run PCA to find the appropriate PCs for dimensionality reduction and then run UMAP/PHATE/tSNE etc. Any advice on which practice is best would be greatly appreciated.

ADD COMMENTlink written 4 months ago by fouerghi2030

Still looking for help! Thank you.

ADD REPLYlink written 3 months ago by fouerghi2030
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1801 users visited in the last hour
_