how to import multiple fastq files from NCBI without using fastq-dump?
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9 weeks ago

Hello I need to import to my server the following dataset:

https://trace.ncbi.nlm.nih.gov/Traces/sra/?study=ERP001736

it consist of 492 fastq files.

I know that I can go to the ERR files thar are available here: https://trace.ncbi.nlm.nih.gov/Traces/study/?acc=ERP001736&o=acc_s%3Aa

and use fastq-dump, but this seems to be the raw data and making quality control over such data can be a waste of time given the fact that I can get the filtered reads into my server directly.

so how can I load such data iteratively using wget or curl ?

additionaly, it can be the situation in which the server's internet falls during the importation. is there a way that wget or curl can retake the download process if something like that happens?

Thanks for reading :)

curl wget multi-samples importing • 111 views
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I assume since the files on first link have the word clean in them you think they are already processed? You could look at the source code for that page (right-click on page --> "view page source" or similar depending on your browser) and parse out all links that have the ftp.sra.ebi.ac.uk URL's. Then use wget and a file with these URL's in to download the data.

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