If 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.
The format of a BioProject ID is PRJNA followed by one to six numbers (e.g., PRJNA291540). The format of a GEO Accession number is GSE followed by one to five numbers (e.g., GSE71578).
The Analyses tab will include an Unaligned reads data node once the data download has started (Figure 3). 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.
If the study is not publicly available in both GEO and ENA, project import will not succeed.
If there is an ENA project, but the FASTQ files are not available through ENA, the project will be created, but data will not be imported.
A variety of other issues and irregularities can cause imports to not succeed or partially succeed, including, but not limited to, a BioProject having multiple associated GSE IDs, incomplete information on the GEO or ENA page, and either the GEO or ENA project not being publicly available.
The Gene Expression Omnibus (GEO) and the European Nucleotide Archive (ENA) are web-accessible public repositories for genomic data and experiments. Access and learn more about their resources at their respective websites:
GEO - https://www.ncbi.nlm.nih.gov/geo/
ENA - https://www.ebi.ac.uk/ena
You can search ENA using the GEO ID (e.g., GSE71578) to check if there is a matching ENA project (Figure 6).
Open the Study result to view the BioProject ID (e.g., PRJNA381606) and a table with information about the samples and files included in the project (Figure 7).