Flow Documentation

Partek Flow Documentation

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SubtitleTextData tab in Partek Flow.
AnchorNameData tab

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SubtitleTextInput FASTQ files for scATAC-Seq data in Flow.
AnchorNameInput FASTQ files

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Convert FASTQ to count 

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SubtitleTextConvert FASTQ by Cell Ranger - ATAC task in Flow.
AnchorNameCell 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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SubtitleTextQA/QC task report for scATAC - Seq data in Flow.
AnchorNameQA/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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SubtitleTextFilter low quality cells in Partek Flow.
AnchorNameFilter cells

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Filter features

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SubtitleTextFilter features in Partek Flow.
AnchorNameFilter features

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Annotate regions

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SubtitleTextTF-IDF normalization for scATAC-Seq in Flow.
AnchorNameNormalization

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To run TF-IDF normalization, 

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SubtitleTextConfigure Graph-based clustering in Flow.
AnchorNameConfigure 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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SubtitleTextComputer biomarkers results in Flow.
AnchorNameComputer 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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