I am a begginer in scRNAseq and researching batch correction methods. I have found and setup Combat, Scanorama, BBKNN and MNN (even though MNN is awfully slow to run at home computer).
I am wondering specifically WHEN is best to run this correction, is there an universally accepted step where batch correction should be applied or is it method dependent?. I have read the best practices guide, which uses Combat and is ran after Normalization and logarithmization. Following batch correction then it is recommented to go with HVG and PCA.
However, other methods like BBKNN requires PCA to be computed in advance…in this case when do you perform HVG? After BBKNN would be my guess but then…PCA will look very different compared to Combat? Unless you run PCA again after BBKNN as well?.
As you see I am a bit confused so if anyone could shed some light it would be appreciated!