Question: I see the following error when demultiplexing my libraries: "[error] bcl2fastq exited with an error. You may have specified an invalid command-line option". How can I continue to demultiplex my data?
Answer: This error can indicate that the samplesheet supplied to mkfastq has a sample index ("barcode") collision. It can happen if the same sample index and lane were specified for multiple samples, or in certain cases where 10x Chromium i7 Multiplex Kit and i7 Multiplex Kit N samples were run on the same flowcell. It is a known issue that certain sample index combinations from these two different kits only differ by two bases-- meaning that it is possible for the sequencer to generate index reads with sequences that are one base away from multiple sample indices.
Please check your samplesheet to verify you do not have duplicate lane-sample index pairs for multiple samples. If there are no duplicates, please run mkfastq with a --barcode-mismatches=0 argument. (The default parameter is --barcode-mismatches=1). This will make bcl2fastq only accept reads that match the sample indices exactly. The small percentage of reads that are a single base away from multiple sample indices will be ignored.
You could also upgrade to most recent version of Cell Ranger which has a clearer message in case sample index collision.