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      • Updating Partek Flow
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      • Dependencies
      • Docker and Docker-compose
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    • Live Training Event Recordings
      • Bulk RNA-Seq Analysis Training
      • Basic scRNA-Seq Analysis & Visualization Training
      • Advanced scRNA-Seq Data Analysis Training
      • Bulk RNA-Seq and ATAC-Seq Integration Training
      • Spatial Transcriptomics Data Analysis Training
      • scRNA and scATAC Data Integration Training
    • Tutorials
      • Creating and Analyzing a Project
        • Creating a New Project
        • The Metadata Tab
        • The Analyses Tab
        • The Log Tab
        • The Project Settings Tab
        • The Attachments Tab
        • Project Management
        • Importing a GEO / ENA project
      • Bulk RNA-Seq
        • Importing the tutorial data set
        • Adding sample attributes
        • Running pre-alignment QA/QC
        • Trimming bases and filtering reads
        • Aligning to a reference genome
        • Running post-alignment QA/QC
        • Quantifying to an annotation model
        • Filtering features
        • Normalizing counts
        • Exploring the data set with PCA
        • Performing differential expression analysis with DESeq2
        • Viewing DESeq2 results and creating a gene list
        • Viewing a dot plot for a gene
        • Visualizing gene expression in Chromosome view
        • Generating a hierarchical clustering heatmap
        • Performing biological interpretation
        • Saving and running a pipeline
      • Analyzing Single Cell RNA-Seq Data
      • Analyzing CITE-Seq Data
        • Importing Feature Barcoding Data
        • Data Processing
        • Dimensionality Reduction and Clustering
        • Classifying Cells
        • Differentially Expressed Proteins and Genes
      • 10x Genomics Visium Spatial Data Analysis
        • Start with pre-processed Space Ranger output files
        • Start with 10x Genomics Visium fastq files
        • Spatial data analysis steps
        • View tissue images
      • 10x Genomics Xenium Data Analysis
        • Import 10x Genomics Xenium Analyzer output
        • Process Xenium data
        • Perform Exploratory analysis
        • Make comparisons using Compute biomarkers and Biological interpretation
      • Single Cell RNA-Seq Analysis (Multiple Samples)
        • Getting started with the tutorial data set
        • Classify cells from multiple samples using t-SNE
        • Compare expression between cell types with multiple samples
      • Analyzing Single Cell ATAC-Seq data
      • Analyzing Illumina Infinium Methylation array data
      • NanoString CosMx Tutorial
        • Importing CosMx data
        • QA/QC, data processing, and dimension reduction
        • Cell typing
        • Classify subpopulations & differential expression analysis
    • User Manual
      • Interface
      • Importing Data
        • SFTP File Transfer Instructions
        • Import single cell data
        • Importing 10x Genomics Matrix Files
        • Importing and Demultiplexing Illumina BCL Files
        • Partek Flow Uploader for Ion Torrent
        • Importing 10x Genomics .bcl Files
        • Import a GEO / ENA project
      • Task Menu
        • Task actions
        • Data summary report
        • QA/QC
          • Pre-alignment QA/QC
          • ERCC Assessment
          • Post-alignment QA/QC
          • Coverage Report
          • Validate Variants
          • Feature distribution
          • Single-cell QA/QC
          • Cell barcode QA/QC
        • Pre-alignment tools
          • Trim bases
          • Trim adapters
          • Filter reads
          • Trim tags
        • Post-alignment tools
          • Filter alignments
          • Convert alignments to unaligned reads
          • Combine alignments
          • Deduplicate UMIs
          • Downscale alignments
        • Annotation/Metadata
          • Annotate cells
          • Annotation report
          • Publish cell attributes to project
          • Attribute report
          • Annotate Visium image
        • Pre-analysis tools
          • Generate group cell counts
          • Pool cells
          • Split matrix
          • Hashtag demultiplexing
          • Merge matrices
          • Descriptive statistics
          • Spot clean
        • Aligners
        • Quantification
          • Quantify to annotation model (Partek E/M)
          • Quantify to transcriptome (Cufflinks)
          • Quantify to reference (Partek E/M)
          • Quantify regions
          • HTSeq
          • Count feature barcodes
          • Salmon
        • Filtering
          • Filter features
          • Filter groups (samples or cells)
          • Filter barcodes
          • Split by attribute
          • Downsample Cells
        • Normalization and scaling
          • Impute low expression
          • Impute missing values
          • Normalization
          • Normalize to baseline
          • Normalize to housekeeping genes
          • Scran deconvolution
          • SCTransform
          • TF-IDF normalization
        • Batch removal
          • General linear model
          • Harmony
          • Seurat3 integration
        • Differential Analysis
          • GSA
          • ANOVA/LIMMA-trend/LIMMA-voom
          • Kruskal-Wallis
          • Detect alt-splicing (ANOVA)
          • DESeq2(R) vs DESeq2
          • Hurdle model
          • Compute biomarkers
          • Transcript Expression Analysis - Cuffdiff
          • Troubleshooting
        • Survival Analysis with Cox regression and Kaplan-Meier analysis - Partek Flow
        • Exploratory Analysis
          • Graph-based Clustering
          • K-means Clustering
          • Compare Clusters
          • PCA
          • t-SNE
          • UMAP
          • Hierarchical Clustering
          • AUCell
          • Find multimodal neighbors
          • SVD
          • CellPhoneDB
        • Trajectory Analysis
          • Trajectory Analysis (Monocle 2)
          • Trajectory Analysis (Monocle 3)
        • Variant Callers
          • SAMtools
          • FreeBayes
          • LoFreq
        • Variant Analysis
          • Fusion Gene Detection
          • Annotate Variants
          • Annotate Variants (SnpEff)
          • Annotate Variants (VEP)
          • Filter Variants
          • Summarize Cohort Mutations
          • Combine Variants
        • Copy Number Analysis (CNVkit)
        • Peak Callers (MACS2)
        • Peak analysis
          • Annotate Peaks
          • Filter peaks
          • Promoter sum matrix
        • Motif Detection
        • Metagenomics
          • Kraken
          • Alpha & beta diversity
          • Choose taxonomic level
        • 10x Genomics
          • Cell Ranger - Gene Expression
          • Cell Ranger - ATAC
          • Space Ranger
          • STARsolo
        • V(D)J Analysis
        • Biological Interpretation
          • Gene Set Enrichment
          • GSEA
        • Correlation
          • Correlation analysis
          • Sample Correlation
          • Similarity matrix
        • Export
        • Classification
        • Feature linkage analysis
      • Data Viewer
      • Visualizations
        • Chromosome View
          • Launching the Chromosome View
          • Navigating Through the View
          • Selecting Data Tracks for Visualization
          • Visualizing the Results Using Data Tracks
          • Annotating the Results
          • Customizing the View
        • Dot Plot
        • Volcano Plot
        • List Generator (Venn Diagram)
        • Sankey Plot
        • Transcription Start Site (TSS) Plot
        • Sources of variation plot
        • Interaction Plots
        • Correlation Plot
        • Pie Chart
        • Histograms
        • Heatmaps
        • PCA, UMAP and tSNE scatter plots
        • Stacked Violin Plot
      • Pipelines
        • Making a Pipeline
        • Running a Pipeline
        • Downloading and Sharing a Pipeline
        • Previewing a Pipeline
        • Deleting a Pipeline
        • Importing a Pipeline
      • Large File Viewer
      • Settings
        • Personal
          • My Profile
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          • Forgot Password
        • System
          • System Information
          • System Preferences
          • LDAP Configuration
        • Components
          • Filter Management
          • Library File Management
            • Library File Management Settings
            • Library File Management Page
            • Selecting an Assembly
            • Library Files
            • Update Library Index
            • Creating an Assembly on the Library File Management Page
            • Adding Library Files on the Library File Management Page
            • Adding a Reference Sequence
            • Adding a Cytoband
            • Adding Reference Aligner Indexes
            • Adding a Gene Set
            • Adding a Variant Annotation Database
            • Adding a SnpEff Variant Database
            • Adding a Variant Effect Predictor (VEP) Database
            • Adding an Annotation Model
            • Adding Aligner Indexes Based on an Annotation Model
            • Adding Library Files from Within a Project
            • Microarray Library Files
            • Adding Prep kit
            • Removing Library Files
          • Option Set Management
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      • Server Management
        • Backing Up the Database
        • System Administrator Guide (Linux)
        • Diagnosing Issues
        • Moving Data
        • Partek Flow Worker Allocator
      • Enterprise Features and Toolkits
        • REST API
          • REST API Command List
      • Microarray Toolkit
        • Importing Custom Microarrays
      • Glossary
    • Webinars
    • Blog Posts
      • How to select the best single cell quality control thresholds
      • Cellular Differentiation Using Trajectory Analysis & Single Cell RNA-Seq Data
      • Spatial transcriptomics—what’s the big deal and why you should do it
      • Detecting differential gene expression in single cell RNA-Seq analysis
      • Batch remover for single cell data
      • How to perform single cell RNA sequencing: exploratory analysis
      • Single Cell Multiomics Analysis: Strategies for Integration
      • Pathway Analysis: ANOVA vs. Enrichment Analysis
      • Studying Immunotherapy with Multiomics: Simultaneous Measurement of Gene and Protein
      • How to Integrate ChIP-Seq and RNA-Seq Data
      • Enjoy Responsibly!
      • To Boldly Go…
      • Get to Know Your Cell
      • Aliens Among Us: How I Analyzed Non-Model Organism Data in Partek Flow
    • White Papers
      • Understanding Reads in RNA-Seq Analysis
      • RNA-Seq Quantification
      • Gene-specific Analysis
      • Gene Set ANOVA
      • Partek Flow Security
      • Single Cell Scaling
      • UMI Deduplication in Partek Flow
      • Mapping error statistics
    • Release Notes
      • Release Notes Archive - Partek Flow 10
  • Partek Genomics Suite
    • Installation Guide
      • Minimum System Requirements
      • Computer Host ID Retrieval
      • Node Locked Installation
        • Windows Installation
        • Macintosh Installation
      • Floating/Locked Floating Installation
        • Linux Installation
          • FlexNet Installation on Linux
        • Installing FlexNet on Windows
        • License Server FAQ's
        • Client Computer Connection to License Server
      • Uninstalling Partek Genomics Suite
      • Updating to Version 7.0
      • License Types
      • Installation FAQs
    • User Manual
      • Lists
        • Importing a text file list
        • Adding annotations to a gene list
        • Tasks available for a gene list
        • Starting with a list of genomic regions
        • Starting with a list of SNPs
        • Importing a BED file
        • Additional options for lists
      • Annotation
      • Hierarchical Clustering Analysis
      • Gene Ontology ANOVA
        • Implementation Details
        • Configuring the GO ANOVA Dialog
        • Performing GO ANOVA
        • GO ANOVA Output
        • GO ANOVA Visualisations
        • Recommended Filters
      • Visualizations
        • Dot Plot
        • Profile Plot
        • XY Plot / Bar Chart
        • Volcano Plot
        • Scatter Plot and MA Plot
        • Sort Rows by Prototype
        • Manhattan Plot
        • Violin Plot
      • Visualizing NGS Data
      • Chromosome View
      • Methylation Workflows
      • Trio/Duo Analysis
      • Association Analysis
      • LOH detection with an allele ratio spreadsheet
      • Import data from Agilent feature extraction software
      • Illumina GenomeStudio Plugin
        • Import gene expression data
        • Import Genotype Data
        • Export CNV data to Illumina GenomeStudio using Partek report plug-in
        • Import data from Illumina GenomeStudio using Partek plug-in
        • Export methylation data to Illumina GenomeStudio using Partek report plug-in
    • Tutorials
      • Gene Expression Analysis
        • Importing Affymetrix CEL files
        • Adding sample information
        • Exploring gene expression data
        • Identifying differentially expressed genes using ANOVA
        • Creating gene lists from ANOVA results
        • Performing hierarchical clustering
        • Adding gene annotations
      • Gene Expression Analysis with Batch Effects
        • Importing the data set
        • Adding an annotation link
        • Exploring the data set with PCA
        • Detect differentially expressed genes with ANOVA
        • Removing batch effects
        • Creating a gene list using the Venn Diagram
        • Hierarchical clustering using a gene list
        • GO enrichment using a gene list
      • Differential Methylation Analysis
        • Import and normalize methylation data
        • Annotate samples
        • Perform data quality analysis and quality control
        • Detect differentially methylated loci
        • Create a marker list
        • Filter loci with the interactive filter
        • Obtain methylation signatures
        • Visualize methylation at each locus
        • Perform gene set and pathway analysis
        • Detect differentially methylated CpG islands
        • Optional: Add UCSC CpG island annotations
        • Optional: Use MethylationEPIC for CNV analysis
        • Optional: Import a Partek Project from Genome Studio
      • Partek Pathway
        • Performing pathway enrichment
        • Analyzing pathway enrichment in Partek Genomics Suite
        • Analyzing pathway enrichment in Partek Pathway
      • Gene Ontology Enrichment
        • Open a zipped project
        • Perform GO enrichment analysis
      • RNA-Seq Analysis
        • Importing aligned reads
        • Adding sample attributes
        • RNA-Seq mRNA quantification
        • Detecting differential expression in RNA-Seq data
        • Creating a gene list with advanced options
        • Visualizing mapped reads with Chromosome View
        • Visualizing differential isoform expression
        • Gene Ontology (GO) Enrichment
        • Analyzing the unexplained regions spreadsheet
      • ChIP-Seq Analysis
        • Importing ChIP-Seq data
        • Quality control for ChIP-Seq samples
        • Detecting peaks and enriched regions in ChIP-Seq data
        • Creating a list of enriched regions
        • Identifying novel and known motifs
        • Finding nearest genomic features
        • Visualizing reads and enriched regions
      • Survival Analysis
        • Kaplan-Meier Survival Analysis
        • Cox Regression Analysis
      • Model Selection Tool
      • Copy Number Analysis
        • Importing Copy Number Data
        • Exploring the data with PCA
        • Creating Copy Number from Allele Intensities
        • Detecting regions with copy number variation
        • Creating a list of regions
        • Finding genes with copy number variation
        • Optional: Additional options for annotating regions
        • Optional: GC wave correction for Affymetrix CEL files
        • Optional: Integrating copy number with LOH and AsCN
      • Loss of Heterozygosity
      • Allele Specific Copy Number
      • Gene Expression - Aging Study
      • miRNA Expression and Integration with Gene Expression
        • Analyze differentially expressed miRNAs
        • Integrate miRNA and Gene Expression data
      • Promoter Tiling Array
      • Human Exon Array
        • Importing Human Exon Array
        • Gene-level Analysis of Exon Array
        • Alt-Splicing Analysis of Exon Array
      • NCBI GEO Importer
    • Webinars
    • White Papers
      • Allele Intensity Import
      • Allele-Specific Copy Number
      • Calculating Genotype Likelihoods
      • ChIP-Seq Peak Detection
      • Detect Regions of Significance
      • Genomic Segmentation
      • Loss of Heterozygosity Analysis
      • Motif Discovery Methods
      • Partek Genomics Suite Security
      • Reads in RNA-Seq
      • RNA-Seq Methods
      • Unpaired Copy Number Estimation
    • Release Notes
    • Version Updates
    • TeamViewer Instructions
  • Getting Help
    • TeamViewer Instructions
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On this page
  • Navigating the file browser to transfer files to the server
  • Associate fastq files for multi-omic data
  • Additional Assistance

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  1. Partek Flow
  2. User Manual

Importing Data

PreviousInterfaceNextSFTP File Transfer Instructions

Last updated 4 months ago

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Partek Flow can import a wide variety of data types including raw counts, matrices, microarray, variant call files as well as unaligned and aligned NGS data.

The following file types are valid and will be recognized by the Partek Flow file browser.

  • bam

  • bcf

  • bcl

  • bgx

  • bpm

  • cbcl

  • CEL

  • csv

  • fa

  • fasta

  • fastq

  • fcs

  • fna

  • fq

  • gz

  • h5ad

  • h5 matrix

  • idat

  • loom

  • mtx

  • probe_tab

  • qual

  • raw

  • rds

  • sam

  • sff

  • sra

  • tar

  • tsv

  • txt

  • vcf

  • zip

In cases where paired end fastq data is present, files will also be automatically recognized and their paired relationship will be maintained throughout the analysis.

Matching on paired end files is based on file names: every character in both file names must match, except for the section that determines whether a file is the first or the second file. For instance, if the first file contains "_R1", "_1", "_F3", "_F5" in the file name, the second file must contain something in the lines with the following: "_R2", "_2", "_F5", "_F5-P2", "_F5-BC", "_R3", "_R5" etc. The identifying section must be separated from the rest of the filename with underscores or dots. If two conflicting identifiers are present then the file is treated as single end. For example, s_1_1 matches s_1_2, as described above. However, s_2_1 does not mate with s_1_2 and the files will be treated as two single-end files.

Apart from paired-end data, files with conventional filename suffixes that indicate that they belong to the same sample are consolidated. These suffixes include:

  • Adapter sequences

    • "bbbbbb" followed by "" or at the end of the file name, where each "b" is "A", "C", "G", or "T"

  • Lane numbers

    • "L###" followed by "" or at the end of the file name, where each "#" is a digit 0 to 9

  • Dates

    • in the form "####-##-##" preceded or followed by a period or underscore

  • Set number

    • of the form "_###" from the end

Navigating the file browser to transfer files to the server

The file browser is used to transfer files to the server so that these files can be added to a project for analysis. If you are importing a Bioproject from GEO/ENA or using URLs for data import, there is no need to transfer the files to the server.

To access the file browser and upload data to the server, use any of these options:

  • from the settings, go to Access management > Transfer files

Using the file browser to transfer files to the server:

  • Do not exit the browser tab or let the computer go to sleep or shut down until the transfer has completed

File size displayed in the table is binary format, not decimal format (e.g. GB displayed in the table is gigibyte not gigabyte. 1 gigibyte is 1,073,741,824 bytes. 1 gigabyte is 1,000,000,000 bytes. 1 gigibyte is 1.074 gigabytes).

Associate fastq files for multi-omic data

There are projects with more than one file type, such as single cell multi-omic assays that generate protein and RNA together. In these cases, files need to be associated with each other if starting in fastq format. If we start with processed data, there is no need to associate these files.

  • Define the type of data the file represents when importing files into the project.

If this step is skipped, the data type can be changed after import by right clicking the data node.

  • After importing both types of data, associate fastqs with the already imported data. (e.g. associate RNA fastqs with ATAC fastqs already imported into Partek Flow.

Additional Assistance

access Transfer files on the Partek® Flow® homepage

within a project, after selecting the file type to transfer, using the transfer files link available within all file import options

Click Transfer files to access the file browser

Drag and drop or click My Device to add files from your machine

Click Browse to modify the Upload directory or create a new folder. The Upload directory should be specified, known, and distinguishable for project file management. You will return to this directory and access the files to import them into a project

To continue to add more files use + Add more in the top right corner. To cancel the process select Cancel in the top left corner

Click Upload to complete the file upload

If you need additional assistance, please visit to submit a help ticket or find phone numbers for regional support.

our support page
SFTP File Transfer Instructions
Sample Table from a Text File
Import single cell data
Importing 10x Genomics Matrix Files
Importing and Demultiplexing Illumina BCL Files
Partek Flow Uploader for Ion Torrent
Importing 10x Genomics .bcl Files
Import a GEO / ENA project
Navigating the file browser to transfer files to the server
Associate fastq files for multi-omic data
Select data type
Change data type
Associate files with this sample