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Once the Genomics production has been picked, users will be asked to create a Reference assembly if it is the first time to run the Cell Ranger - Gene Expression task in Flow (Figure 2). In Partek Flow, we will use Cell Ranger ARC 2.0.0 to create reference assembly for all 10x Genomics analysis pipelines. To create and use a reference assembly, Cell Ranger ARC requires a reference genome sequence (FASTA file) and gene annotations (GTF file).

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While for Feature Barcode data, there are more information needed besides reference assembly. An additional section of Protein has been added to the interface if Single cell gene expression + Cell surface protein has been selected for Feature Barcode data (Figure 5). Users need firstly push the button Select data node and select the correct data for feature of antibody capture or protein in the newly popped-out a new pop-up window (top right, Figure 5). Then users need to upload the feature reference file (.csv) prepared for their datasets. A Feature Reference CSV file declares the molecule structure and unique Feature Barcode sequence of each feature present in the experiment. It should include at least six columns: id, name, read, pattern, sequence and feature_type. An example of TotalSeq™-B Feature Reference CSV has been linked here. Users can download it by clicking the link and use it as a template for their own data. But for more details, please refer to 10x Genomics webpage[4].

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Memory limit (GB): Restricts Cell Ranger - Gene Expression to use specified amount of memory (in GB) to execute pipeline stages. 

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