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SubtitleText | Data tab in Partek Flow. |
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AnchorName | Data tab |
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SubtitleText | Input FASTQ files for scATAC-Seq data in Flow. |
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AnchorName | Input FASTQ files |
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Convert FASTQ to count
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SubtitleText | Convert FASTQ by Cell Ranger - ATAC task in Flow. |
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AnchorName | Cell Ranger - ATAC |
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To learn more about how to run Cell Ranger - ATAC task in Flow, please refer to our online documentation.
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SubtitleText | QA/QC task report for scATAC - Seq data in Flow. |
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AnchorName | QA/QC task report |
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The Single cell QA/QC report includes interactive violin plots showing the value of every cell in the project on several quality measures (Figure 6).
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SubtitleText | Filter low quality cells in Partek Flow. |
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AnchorName | Filter cells |
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Filter features
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SubtitleText | Filter features in Partek Flow. |
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AnchorName | Filter features |
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Annotate regions
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SubtitleText | TF-IDF normalization for scATAC-Seq in Flow. |
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AnchorName | Normalization |
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To run TF-IDF normalization,
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SubtitleText | Configure Graph-based clustering in Flow. |
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AnchorName | Configure Graph-based clustering |
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A new Graph-based clusters data and a Biomarkers data node will be generated.
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SubtitleText | Computer biomarkers results in Flow. |
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AnchorName | Computer biomarkers results |
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UMAP
Similar to t-SNE, Uniform Manifold Approximation and Projection (UMAP) is a dimensional reduction technique. UMAP aims to preserve the essential high-dimensional structure and present it in a low-dimensional representation. UMAP is particularly useful for visually identifying groups of similar samples or cells in large high-dimensional data sets.
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