Dear all,
'd appreciate also having your suggestions on the following case of scRNAseq analysis with Seurat 3.1. ; the question is : what analysis strategy would you recommend (described below) ?
shall we have 4 batches of scRNA-seq data of these experiments :
WT_batch1, WT_batch2, A_batch1, A_batch2
WT_batch3, WT_batch4, B_batch3, B_batch4
what is the optimal way to analyze the data-sets ? Several analysis strategies are possible :
STRATEGY A.
1. to use CELLRANGER AGGR (with NORMALIZATION = TRUE) on :
WT_batch1, WT_batch2 : to produce WT_batch_1_2
A_batch1, A_batch2 : to produce A_batch_1_2
WT_batch3, WT_batch4 : to produce WT_batch_3_4
B_batch3, B_batch4 : to produce B_batch_3_4**
2. and to follow the descriptions of SEURAT pipelines with LIGER, HARMONY, CONOS, fastMNN (below) on WT_batch_1_2, WT_batch_3_4, A_batch_1_2, B_batch_3_4 :
STRATEGY B.
1. to use SEURAT MERGE function in order to have all the data (WT_batch1, WT_batch2, A_batch1, A_batch2, WT_batch3, WT_batch4, B_batch3, B_batch4) in a large MATRIX
2. follow the tutorials on SCTRANSFORM, or reciprocal_PCA in https://satijalab.org/seurat/v3.1/integration.html
however, when I call the function FindMarkers in SEURAT (FindMarkers(object, ident.1, ident.2), how shall I specify the REPLICATES in ident.1 and in ident.2 ?
Any other analysis strategy ? Any suggestions, comments would be very welcome ! Thanks a lot !
-- bogdan
Cross-posted: https://support.bioconductor.org/p/127811/
Also cross posted here: https://bioinformatics.stackexchange.com/questions/11248/analysis-of-multiple-time-points-2-replicates-of-scrna-seq
Bogdan : Please stop posting these in multiple forums. It is rude and annoys people across forums.
Hi gentlemen, sorry ... i was hoping to learn from the experience of people from multiple forums ;)