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Although the index files (I1 or I2) are optional, we encourage users to include all of the FASTQs in the table (Figure 9) while importing data for Cell Ranger - ATAC.   

Import The import of ATAC FASTQ files are as straightforward as the (sc)RNA-seq Seq data. However, we have need to associate the two different types of data together for 10x multiome ATAC + Gene Expression data.  It This includes two steps: 1). Import the ATAC FASTQ files in the new page after clicking on the "Automatically create samples from files" in Data tab (Figure 10A) and select the data type, as ATAC-Seq, from the dropdown list (Figure 10B) to be ATAC-Seq. 2). Move back to the Data tab and display all of the files by clicking on the Show data files button at the bottom left of Sample name table. Then go clicking click the green + button button Image Added (Figure 10C) to add RNA FASTQs to the same sample. Similarly, we will select the data type from the dropdown (mRNA) before we finish the import process by clicking on the Associate file button (Figure 10D). 

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