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At present, the I1 file of ATAC FASTQs has to be included for both Flow Cell Ranger - ATAC tasks: ATAC only and the Multiome ATAC + Gene Expression (Figure 9). However, index files are not needed Although index file I1 is optional in Flow for gene expression FASTQs while processing multiomics data. We encourage users to include all the FASTQs in the table (Figure 9) while importing data for Cell Ranger - ATAC.   

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