How to import a study from GEO / ENA

Partek^® Flow^® supports single cell data analysis in count matrix text format. Each matrix text file is assumed to represent on sample, each value in the matrix represents expression value of a feature (e.g. a gene, or a transcript) in a cell. The expression value can be raw count, or normalized count. The requirment of the format of each text file should be the same as count matrix data.

To import a sample during import data, choose Import single cell data option (Figure 1)

Specify text file location, only one text file (in other words one sample) can be imported at once, preview of the file will be displayed, configuration of the file format is the same as Import count matrix data. In addition, you need to specify Sample information and Gene deduplication method (Figure 2).

Click Finish, the sample will be imported,  on the data tab, number of cells in the sample will  be displayed.

To import multiple samples, repeat the above steps by clicking Import data on the data tabIf a project is publicly available in the Gene Expression Omnibus (GEO) and European Nucleotide Archive (ENA) databases, you can import associated FASTQ files, sample attributes, and project details automatically into Partek Flow.

• On the Homepage click New Project to create a project and give the project a name

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• Click Add data

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• Select fastq as the file type after choosing between Single cell or Bulk as the assay types

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• Choose GEO / ENA 
• Enter the BioProject ID of the data set you would like to download. The format of a BioProject ID is PRJNA followed by one to six numbers (e.g. PRJNA291540)

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A GEO ID can also be used in the format GSE followed by one to five numbers (e.g. GSE71578). 

• Click Finish

Imported projects from GEO / ENA

Common Issues

FAQ

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