Question: I resequenced my single cell 3' library on a different flowcell to increase my sequencing saturation. Can I combine data from multiple sequencing runs for the same 10x library?
Answer: If you resequenced the same library (corresponding to the same channel of a Chromium chip) on different lanes of the same flowcell, or on different flowcells, to increase depth of coverage or for some other reason, you can specify multiple paths to the different directories containing these FASTQ files (after demultiplexing) as a comma-separated list to the --fastqs argument in cellranger count.
For example, if you have two directories of FASTQs (/home/fastqs/run1 and /home/fastqs/run2) from two different sequencing runs, you would specify them in your command line as follows:
cellranger count --id=unique_job_id --transcriptome=path/to/reference --fastqs=/home/fastqs/run1,/home/fastqs/run2
If there are multiple sample name prefixes that correspond to different libraries in that directory, be sure to use the --sample option as well. For more information on combining multiple sequencing runs in Cell Ranger please see Specifying Input FASTQ Files for 10x Pipelines.