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Question: extract reads with fastq-dump tool
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gravatar for denisem12
2.1 years ago by
denisem12 • 10
denisem12 • 10 wrote:

I'm trying to extract reads from sra files but it says that one of the files is a new dataset and therefore is not available yet. However I could downloaded it to my computer. But for some reason doesn't let me look for it through the fastq-dump tool even if I already uploaded that dataset on galaxy.

any help?
rna-seq galaxy • 965 views
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written 2.1 years ago by denisem12 • 10
1
gravatar for Mo Heydarian
2.1 years ago by
Mo Heydarian ♦ 830
United States
Mo Heydarian ♦ 830 wrote:

Hello, A bit more information may help in resolving this issue. Are you using useGalaxy.org or another instance? Do you see this behavior when extracting reads using a single SRR ID or a list if SRR IDs?

Cheers, Mo Heydarian, Galaxy Team
ADD COMMENT • link written 2.1 years ago by Mo Heydarian ♦ 830

Hello, I used 2 different SRR IDs and told me the same thing. Then I used 2 other SRR IDs and it worked perfectly.

And yes I'm using galaxy.org

Thanks!

Denise

ADD REPLY • link written 2.1 years ago by denisem12 • 10
1

Have you tried to re-import the data of the first two SRR IDs that were troublesome?

ADD REPLY • link written 2.1 years ago by Mo Heydarian ♦ 830

I re run them today and I just got the results. Don't know why yesterday wasn't working.

thanks a lot for your help!

Denise

ADD REPLY • link written 2.1 years ago by denisem12 • 10
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