Question: I am starting with a BAM file produced by Cell Ranger or Long Ranger, how can I convert this back into FASTQ format so I can re-run the pipeline?
Answer: We offer a tool called bamtofastq (not to be confused with the one bundled with bedtools) for converting 10x BAMs produced by cellranger or longranger back to FASTQ files that can be used as inputs to re-run analysis. The FASTQs will be emitted into a directory structure that is compatible with the directories created by the mkfastq tool.