Question: Does Cell Ranger need the I1 FASTQ file to run?
Answer: In most cases, no. If the libraries were made using 5' gene expression, V(D)J assay, or 3' gene expression v2+ chemistry, you do not need I1 FASTQ files for running Cell Ranger. This is because the 10x Genomics barcode is in R1 FASTQ files.
However, if you are using data from libraries made with 3'v1 chemistry (e.g., analyzing published or legacy datasets), you will need the I1 files because they contain the 10x Genomics barcode.