Dear all, 

i am writing to ask please for your suggestions about the appropriate use of CELLRANGER AGGR function in the following context  : 

we do have 2 experimental replicates for a WT and DISEASE mice : 

-- WT_replicate1

-- WT_replicate2


-- DIS_replicate1

-- DIS_replicate2

in order to combine the replicates, shall we just use CELLRANGER AGGR, or shall we just put the fastq files in the same folders i.e. 

the fastq files of  *WT_replicate1, WT_replicate2* in a folder, 

and 

the fastq files of  *DIS_replicate1, DIS_replicate2* in another folder ?

thanks a lot, 

bogdan 
You should not process the FASTQs together, because cell barcodes will clash. So you should process them separately. I would not recommend merging the replicates after processing, information about variance within condition will be useful and important for downstream analysis. If you do aggregate the datasets, you should be aware that the aggr function performs a normalization of the data. In the kallisto|bustools workflow we have a [tutorial][1] for aggregation that allows you to explore other normalizations. 

  [1]: https://www.kallistobus.tools/aggr_tutorial.html