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Downloading multiple SRA files as FASTQ files using SRA Toolkit

That is a classical problem where the folder containing the binary of the tool is not in PATH, see for example https://askubuntu.com/questions/109381/how-to-add-path-of-a-program-to-path-environment-...
ATpoint's user avatar
  • 1,326
1 vote
Accepted

How to download Sequencing data on Windows using SRA toolkit?

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 ...
Sanjukta Ghosh's user avatar
1 vote

ZIP the fasterq-dump files in loop

I tried this and it worked ...
Shradha Sharma's user avatar
1 vote

ZIP the fasterq-dump files in loop

Haven't tried, but I believe you may add -Z to fasterq-dump and remove -k ${i} from gzip. In addition, I would recommend the ...
user172818's user avatar
  • 6,535

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