Question: How to download oxford nanopore sequencing fast5 files from SRA
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gravatar for va90
7 months ago by
va9010
va9010 wrote:

Hi,

I am trying to download direct RNA seq data produced by oxford nanopore sequencing from SRA (SRP174366). I know how to use sratoolkit prefetch or fastq-dump to download fastq files, but I do not know how to download nanopore fast5 files from SRA?

Any help would be much appreciated,

Thanks, Vahid.

rna-seq • 639 views
ADD COMMENTlink modified 7 months ago by genomax85k • written 7 months ago by va9010
0
gravatar for genomax
7 months ago by
genomax85k
United States
genomax85k wrote:

If you go to the SRA record of an individual accession from the project link that you posted above, you can click on the run ID and finally get to the Data Access tab on the new page that opens. You will find data in original fast5 format under relevant section at bottom of that tab. There are links to AWS/GCP. You can use the AWS links with wget/curl to download the data to your local server. If you can use google compute then the link for the data in google storage is also available.

ADD COMMENTlink modified 7 months ago • written 7 months ago by genomax85k
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