SRA reads into Galaxy: Study to Accessions

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PRJNA1096305 this is SRA datasets and i want to analyse this single cell data to identify the subsets of neutrophil. How will I do it

I am new to RNA-sequencing analysis and have just started with a dataset but not able to get the data as it is a SRA dataset and I am not getting this file format ( :laughing: ).

I was then keen to get a picture of neutrophil subsets and what is the expression level of CD177 and IL17 along with PNMT enzymes in this subsets. what was up and down regulated in the treated sample.

Or is there a better way of doing this?

Happy to post my history if this all appears nonsense.

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Welcome @Rambha_Jha

To map from the study identifier PRJNA1096305 to the fastq SRX accession identifiers, and get the data organized with nice sample labels, please see this tutorial. → Hands-on: Rule Based Uploader / Rule Based Uploader / Using Galaxy and Managing your Data

You’ll be starting with a query like this one (first step in the tutorial). → https://www.ebi.ac.uk/ena/browser/text-search?query=PRJNA1096305

This will get all samples into your history! Be sure to first toggle to use the extended 1 TB storage to place the raw reads into, as this will ensure your 250 GB permanent storage can be reserved for your results. → How to access your Self Serve extended data storage at UseGalaxy servers! - #2 by jennaj

Once your storage is set up, and your reads are in collection folders in a history, consider exploring our Single Cell RNA-seq tutorials and workflows! Any can be imported and customized.

Hope this helps to get you started! :slight_smile: