Question: 10x has moved to dual indexed libraries which are now supported by 10x software such as "cellranger mkfastq". I still have single indexed libraries. Can I still use Cell Ranger to demultiplex them ?
Answer: Yes, cellranger mkfastq supports single-indexed and dual-indexed flowcells. It will select the appropriate mode depending on the sample indexes used, and enable index-hopping filtering automatically for dual-indexed flowcells. For example, with the Dual Index Kit TT Set A, well A1 can be specified in the samplesheet as SI-TT-A1, and cellranger mkfastq will recognize the i7 and i5 indices as
AGTGTTACCT, respectively. Similarly for Single Index Kit T Set A, well A1 can be specified in the samplesheet as SI-GA-A1, and cellranger mkfastq will recognize the four i7 indexes GGTTTACT, CTAAACGG, TCGGCGTC, and AACCGTAA and merge the resulting FASTQ files.