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fastq-dump a whole "SRP" project? #2

olgabot opened this issue Jul 22, 2014 · 1 comment

fastq-dump a whole "SRP" project? #2

olgabot opened this issue Jul 22, 2014 · 1 comment


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@olgabot olgabot commented Jul 22, 2014

Is it possible to use bionode-sra to fastq-dump a whole project? For example, SRP027537 (aka GSE48968) has approximately 2500 samples and it would be amazing if it was possible to do:

fastq-dump SRP027537

And get all the fastq and metadata files.

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@bmpvieira bmpvieira commented Apr 4, 2015

I believe this was answered by email and we forgot to close this.
The answer was yes, with:
bionode-ncbi download sra SRP027537 | bionode-sra fastq-dump -

@bmpvieira bmpvieira closed this Apr 4, 2015
@bmpvieira bmpvieira self-assigned this Apr 5, 2017
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