Hi my friends. I have a paired-end data (PRJNA998059) I wanna analyze it with GALAXY. However, when I wanna deliver it from GEO NCBI site to galaxy I get this error “Tool ‘sra_source’ does not exist.” Is there any solution? or any other way which I can to upload the whole dataset ? My dataset has 8 samples. I tried the tool GETdata but this tool cannot the whole dataset.
Hi, @Atefeh_Bahmei
PRJNA998059 is accession number for the study: https://www.ebi.ac.uk/ena/browser/view/PRJNA998059
Try run accessions (SRRxxxx).
You can push data from ENA to Galaxy servers. Select a proper Galaxy server and click at Galaxy links. Or create list of accession numbers and import data using Faster Download and Extract Reads in FASTQ format from NCBI SRA
Kind regards,
Igor
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This tutorial has an example of what @igor is suggesting. It walks through how to get from a study identifier to the included accession identifiers through to getting the data organized and tagged inside of Galaxy.
- Hands-on: Rule Based Uploader / Rule Based Uploader / Using Galaxy and Managing your Data
- With more examples in these tutorials → Using Galaxy and Managing your Data / Tutorial List plus several of the domain specific tutorials.
- And our production quality workflows available here → https://iwc.galaxyproject.org/
Let us know how this goes! The first time using the rule builder can be a bit confusing, but after that you’ll be able to do this really quickly to prepare even really large batches data before launching your workflow. 