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This guide illustrates how to process FASTQ files produced using the 10x Genomics Chromium Single Cell ATAC assay to obtain a Single cell counts data node, which is the starting point for analysis of single-cell ATAC experiments.

If you are new to Partek FlowPartek® Flow®, please see Getting Started with Your Partek Flow Hosted Trial for information about data transfer and import and Creating and Analyzing a Project for information about the Partek Flow user interface.  

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We recommend uploading your FASTQ files (fastq.gz) to a folder on the your Partek® Flow® server before importing them into a project. Data files can be transferred into Flow from the Home page by clicking the Transfer file button (Figure 1). Following the instruction In Figure 1 to complete the data transfer. Users have the option to change the Upload directory by clicking the Browse button and either select another existing directory or create a new directory. 

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Nucleosome signal: calculated per single cell, and quantify which quantifies the approximate ratio of mononucleosomal to nucleosome-free fragments. Nucleosome banding pattern: The histogram of DNA fragment sizes (determined from the paired-end sequencing reads) should exhibit a strong nucleosome banding pattern corresponding which corresponds to the length of DNA wrapped around a single nucleosome.

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