Question: When running cellranger mkfastq I get the following error: "[error] Barcode out of bounds (I1:0-14)". How can I solve this?
Answer: This error typically occurs when a 10x single-cell 3', 5', V(D)J or feature barcoding library is run in an unsupported dual indexed configuration (with >14 bp on the i5 index). Deviating from our sequencing recommendations in this manner causes Cell Ranger to misdetect the chemistry as our original dual-indexed v1 chemistry. Please note that our current 3' and 5' GEX libraries are supported in single index mode only:
To work around this error, you will need to demultiplex with bcl2fastq directly. There are detailed instructions for using bcl2fastq directly on our support site here.