Question: No Galaxy Links in EBI SRA - Now what?
gravatar for mmfansler
3.4 years ago by
United States
mmfansler0 wrote:

I am trying to import SRA data (SRR1725164) to Galaxy using the Get Data > EBI SRA tool.  However, the page for the run does not show any links under the fastq (galaxy) column.  I assume that is where I would normally find a way to import (this is my first time using this).  Since there is nothing there, how do I proceed?

I have the SRA Toolkit and am able to (slowly) download the file with fastq-dump, however, the file is huge and I think my internet connection is not going to be stable and fast enough to upload a >10GB file to Galaxy.

What are my options?  Also, do I need to take any additional steps because the data is paired?

If context matters at all, I am hoping to run de novo assembly on this transcriptome data.

rna-seq sra get-data fastq • 1.1k views
ADD COMMENTlink modified 3.4 years ago by Jennifer Hillman Jackson25k • written 3.4 years ago by mmfansler0
gravatar for Jennifer Hillman Jackson
3.4 years ago by
United States
Jennifer Hillman Jackson25k wrote:


For this experiment, I appears that SRI does not have sequences available at all through the web page. If you are able to download it using alternate methods, maybe send their help desk an email and ask why this is missing. Could be a simple mistake. 

You can load data up to 50 GB per file using the FTP upload method. If the upload should fail at some point due to a network issue, the load can be resumed. Try using Filezilla.

Best, Jen, Galaxy team

ADD COMMENTlink modified 3.4 years ago • written 3.4 years ago by Jennifer Hillman Jackson25k
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