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I have downloaded and installed the SRA toolkit, but there seems to be no online material on how to download SRR files using the SRA toolkit on Windows.

All online materials are Ubuntu or Linux based.

Is there some obvious resource that I am missing?

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  • $\begingroup$ Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking. $\endgroup$
    – Community Bot
    Dec 8, 2023 at 17:01

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I found a solution to this problem.

After having installed SRA toolkit:

prefetch -v SRR9....1

this helps download the SRA file.

Then to extract it as FASTAQ

fasterq-dump SRR9....1

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  • $\begingroup$ That just postpones the problem. Now you need to align these files, tell me a single popular Widows aligner. $\endgroup$
    – ATpoint
    Dec 11, 2023 at 8:17
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    $\begingroup$ @ATpoint clustal? Please try and make your comments helpful instead of just snide. Of course you cannot seriously do bioinformatics if you just use Windows, but people who only dabble might be able to get away with it, and the specific example of alignment tools is a bad one. $\endgroup$
    – terdon
    Dec 11, 2023 at 10:41

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