What would be the equivalent fasterq-dump options?

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4.0 years ago

C_sinensis ▴ 30

I have been running the following command to convert SRA files:

fastq-dump -F --gzip --readids --split-files

And I want to transition to fasterq-dump. Which would be the equivalent command? I think it is(given that fasterq-dump doesnt give the option to compress the files):

fasterq-dump -S --include-technical

But I wanted to make sure! Thank you!

fasterq-dump • 3.1k views

ADD COMMENT • link 4.0 years ago by C_sinensis ▴ 30

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alternatively you can download from ENA , they offer direct fastq download (bonus tip, you can get the download cmdlines using sra-explorer website )

ADD REPLY • link 4.0 years ago by lieven.sterck 15k

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File compression options (--gzip or --bzip2) are not available in fasterq-dump

ADD REPLY • link 4.0 years ago by Renesh ★ 2.2k

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Thanks for your reply! Yes, I know I wanted to have the equivalent command EXCEPT the compression. Thanks!

ADD REPLY • link 4.0 years ago by C_sinensis ▴ 30

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