Question: Should I trim the reads in my FASTQ files before running the pipeline?
Answer: Preprocessing of FASTQ data before running any of the 10x Genomics pipelines is not necessary. Furthermore, it is discouraged. Preprocessing that removes sequence (such as quality trimming) can destroy the barcodes leaving you with regular short reads in the case of Supernova and Long Ranger. All of the 10x Genomics pipelines perform the required preprocessing.