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If a project is publicly available in the Gene Expression Omnibus (GEO) and European Nucleotide Archive (ENA) databases, you can import associated FASTQ files , and sample attributes , and project details automatically into Partek Flow.
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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
The data tab will be populated with sample information. Sample names will be GSM IDs for each sample. Attributes and attribute levels are drawn from the GEO sample characteristics information.
GEO import populates the data tab.
Project details are added to the Project settings tab (Figure 4). The project name is the first 54 characters taken from the BioProject ID title. The project description is the BioProject description with the GEO ID and BioProject IDs appended.
The Analyses tab will include an Unaligned reads data node once the data download has started (Figure 5). It may take a while for the download to complete depending on the size of the data. FASTQ files are downloaded from the ENA BioProject page.
- FASTQ files will be added as an Unaligned reads data node in the Analyses tab
Common Issues
Error Message - The project did not yield any data. Double-check the project ID, or try importing the data manually
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