Question: I am starting with a BAM file produced by one of 10x software pipelines. 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 BAM files produced by 10x software 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.
If you are converting a BAM file that contains gene expression and feature barcoding data, please see this article for how to interpret the output directories: How do I find out which fastq files belong to which library in 10x bamtofastq output folders?