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 :
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,
the fastq files of DIS_replicate1, DIS_replicate2 in another folder ?
thanks a lot,