Question: Does Cell Ranger need the I1 FASTQ file to run?
Answer: In most cases, no. If the libraries were made using v2, v3 or v3.1 chemistry for 3' GEX, or v1 or v1.1 chemistry for 5' gene expression and V(D)J libraries, you don't need the I1 file from
mkfastq. For v2, v3 or v3.1 3' gene expression libraries, the barcode is attached to R1.
The exception for Cell Ranger is if you are using data from libraries made with v1 chemistry then you will need the I1 files because they contain the 10x barcode. This is most likely to come into play when analyzing published or legacy datasets.