I'm using cellranger count on 10X generated raw fastq files to get a count table. But I'm confused if I should do any QC step before using cellranger count? Or if there are QC steps included in cellranger count?
I didn't see QC instruction in the cellranger instruction page, but really want to make sure I did everything correctly.
cellranger applies basic QC to remove obviously empty droplets and dead cells and will generate flags in the summary report for each sample if there are issues with alignment, cell numbers, etc. There is no need to do any other QC prior to running cellranger.
You will, however, want to perform QC on your counts matrices to remove dead cells, empty droplets, and multiplets with increased stringency. I recommend reading through the OSCA book for background and examples.