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Question: sra data from ncbi
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gravatar for 1603.neha
2.6 years ago by
1603.neha • 70
1603.neha • 70 wrote:

hi on clicking the link get data- ebi sra i am directed to the ebi website. after finding my sra file how do i get back to galaxy to continue with my analysis. how do i import almost 100 sra files in galaxy for extracting their fastaq sequences.
rna-seq • 2.4k views
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modified 2.6 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.6 years ago by 1603.neha • 70
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gravatar for Jennifer Hillman Jackson
2.6 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Using the Get Data EBI SRA tool, the idea is to browse for the data and then load it into Galaxy by clicking on the appropriate link. This is one file at a time. The data is loaded into Galaxy and your browser will return there automatically. https://wiki.galaxyproject.org/Support#Get_Data:__EBI-SRA

Another way to extract the data, if you know the accession(s) already, is to use the tools in the group NCBI SRA Tools.

Thanks, Jen, Galaxy team
ADD COMMENT • link written 2.6 years ago by Jennifer Hillman Jackson ♦ 25k

Hello, because I could not download the dataset via Get Data EBI SRA tool I installed NCBI SRA Tools into my local galaxy instance.

I generated the list of accession numbers using "Accession List" option form the "SRA RUN Selector" page. When I feed the "Download and Extract Reads in FASTA/Q format from NCBI SRA (Galaxy Version 2.8.1.3)" tool with the accession list I got two empty outputs namely "Single-end data (fastq-dump)" and "paired-end data (fastq-dump)".

Kindly help Thank you

ADD REPLY • link written 12 months ago by mohancm89 • 0

If I use the same tool with single accession number I get the following error

Fatal error: Exit code 3 () 2017-11-15T10:17:07 vdb-config.2.8.1 err: condition violated while updating node - Warning: normally this application should not be run as root/superuser 2017-11-15T10:17:07 prefetch.2.8.1 err: path not found while resolving tree within virtual file system module - 'SRR1029672' cannot be found.

ADD REPLY • link written 12 months ago by mohancm89 • 0

are there any changes that I have to make in the config/galaxy.ini?

ADD REPLY • link written 12 months ago by mohancm89 • 0
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