How to get fastq files of SRA in Galaxy
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3.3 years ago

I need to do a Rna seq on SRP152983, I need to get the fastq files of a number of samples in that SRA, is it possible for me to get it as a collection or do I have to get the fastq files separately for each one of them?

RNA-Seq next-gen sequencing • 5.3k views
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3.3 years ago
Ridha ▴ 130

Hello there! There are multiple methods to get your SRA data to Galaxy:

1) download fastq files to your computre from sra database and upload them manually to galaxy

2) Use the tool download and extract reads in FAST/Q format from NCBI SRA (check this video)

3) Using EBI-SRA tool in galaxy (check this video)

4) Another method which I like and recommend(and I think this is what you are looking for) because it is easier by directly importing data from SRA as collection datatype( very handy especially if you are uploading fastq files that is paired-end). Steps to do this: 1) Go to GEO website using your GSE accession ID.

2) Click on SRA Run Selector ( you see it below in the page)

3)You should see all samples of the experiments or runs. Choose the samples you want from the experiment and click on galaxy from the select window.

4) You will be transferred directly to galaxy server and your data will be uploaded automatically.

Good luck!

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Hello Ridha, thanks for your suggestion, it was very useful for me

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Happy to help anytime. Good luck!

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