Here is the procedure I am following to do scRNA-Seq analysis. Can anyone please suggest to me whether it is correct or wrong?
I have the fastq files for each sample name listed in the following format
[Sample Name]_S1_L00[Lane Number]_[Read Type]_001.fastq.gz For example, the sample name 1011 is in different runs i.e., in run # FGC2121 and lane L001 there is a fastq file 1011_S1_L001_R1_001.fastq.gz and in run # FGC2133 and lane L005 there is another fastq file 1011_S1_L005_R1_001.fastq.gz
For each sample name, I am running cellranger count on each run-lane separately. In other words, I am running run # FGC2121 first and run # FGC2133 and so on.
My first question is if I can run the cellranger aggr function to merge the outputs of different runs for a sample name.
The second question is if I need to run cellranger aggr function again if I want to aggregate different sample names. For ex, aggregation of samples 1011 1022 etc which are different Controls or cases.
I greatly appreciate your suggestions.
