The tool 'sra_source' is not available in Galaxy, which explains the error you encountered when attempting to transfer the data directly from the GEO NCBI site. PRJNA998059 is the BioProject accession for the study "Downregulation of UBA1 Expression in Myelodysplastic Syndrome" in Mus musculus, and it contains eight RNA-Seq samples from mouse bone marrow LSK cells treated with TAK-243 or vehicle control. The individual run accessions are as follows:
- SRR25406677: TAK-243 sample 1
- SRR25406676: TAK-243 sample 2
- SRR25406675: TAK-243 sample 3
- SRR25406674: TAK-243 sample 4
- SRR25406681: Vehicle control 1
- SRR25406680: Vehicle control 2
- SRR25406679: Vehicle control 3
- SRR25406678: Vehicle control 4
To upload the entire dataset, use the "Faster Download and Extract Reads in FASTQ format from NCBI SRA" tool available under the "Get Data" section in Galaxy. This tool replaces older methods and can handle multiple accessions.
First, create a new text file in Galaxy (or upload one from your computer) containing the eight SRR accessions, one per line, without headers:
SRR25406677
SRR25406676
SRR25406675
SRR25406674
SRR25406681
SRR25406680
SRR25406679
SRR25406678
In the tool interface, select "Paired-end" for your data type, then choose "Uploaded file" for the accession list and select your text file. Set "Output as Collection" to yes if you want the files organized automatically. Execute the tool; it will download the data from NCBI SRA and extract it into FASTQ format.
If you wish to separate the treatments, create two separate accession lists (one for TAK-243 samples, one for vehicle controls) and run the tool twice to generate distinct collections.
This approach bypasses the GETdata tool limitations and imports all eight samples directly within Galaxy.
Kevin
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