In single cell RNA-seq, do we perform regular quality checks and adapter trimming before using cellranger?

Question

[mrj]

In single cell RNA-seq, do we perform regular quality checks and adapter trimming (just like in regular RNA-seq) before using cellranger?

Answer 1

[colindaven]

No. Indeed, you can't do it, because CellRanger takes a runfolder, not FASTQ files, as the default input and performs the demultiplexing itself.

Of course, you can demux yourself and run QC on a big unassigned FASTQ, which might help if the run was very suboptimal, but in general the stats from and post CellRanger are what you want.

[mrj]

Thank you for the answer