Regarding cellranger count and aggr functions
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
L001 there is a
1011_S1_L001_R1_001.fastq.gz and in
run # FGC2133 and
L005 there is another
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
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
1022 etc which are different Controls or cases.
I greatly appreciate your suggestions.
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