Question: I have a multiplexed Flex library with multiple samples in one pool and am interested in getting the FASTQ files by sample for data sharing purposes or submission to public databases (e.g. GEO). Is there a way to obtain the individual FASTQ files for each of the samples?
Answer: The way to get FASTQs by sample from a multiplexed Flex library is to first run cellranger multi on the library FASTQ files to demultiplex the samples and obtain the sample_alignments.bam files for each sample (see cellranger multi output structure here). Then you can run the program bamtofastq on the BAM files to obtain FASTQs per sample. Please refer to the article here for more information on bamtofastq: https://www.10xgenomics.com/support/software/cell-ranger/latest/miscellaneous/cr-bamtofastq and our article here for more information on BAM files: https://www.10xgenomics.com/support/software/cell-ranger/latest/analysis/outputs/cr-outputs-bam