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If users have converted FASTQ outside of Partek, Flow has the importer available for count matrix (Figure 8A). Files that Flow will need to complete the import includes: filtered_feature_bc_matrix.h5, per_barcode_metrics.csv, peaks.bed, fragments.tsv.gz.tbi, fragments.tsv.gz. Those files usually could be found in the outs/ subdirectory within the pipeline output directory (Figure 8B). scATAC-seq is complicated, unlike RNA-seq - if peak calling was performed on each sample/dataset independently, the peaks are unlikely to be exactly the same. We therefore need to create a common set of peaks across all the samples/datasets to be merged. The datasets combination in Flow is performed during data import - therefore it needs all samples/datasets to be imported at one time, not separately. Please click the green + button to add more samples (Figure8A).

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