Question

Error occured when converting .SRA to FASTQ

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10.0 years ago

xuzbnu • 0

State as in title, the system returns following message:

data corrupt while validating header within database module- failed to open '....... .sra '

Really appreciate any help!!!!!!

software-error alignment sequencing • 2.4k views

ADD COMMENT • link updated 2.6 years ago by Ram 43k • written 10.0 years ago by xuzbnu • 0

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Have you tried redownloading it?

ADD REPLY • link 10.0 years ago by Devon Ryan 104k

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What "system"? What software? Please be more specific.

ADD REPLY • link 10.0 years ago by Neilfws 49k

Ram · Answer 1 · 2014-04-22

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10.0 years ago

Xingyu Yang ▴ 280

In the recent version of sratools, you don't even need to download the sra file. Just

fastq-dump SRAxxxx

You will get the fastq files you want.

ADD COMMENT • link updated 4.3 years ago by Ram 43k • written 10.0 years ago by Xingyu Yang ▴ 280

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That's a nice feature I never knew about, thanks!

ADD REPLY • link 10.0 years ago by Devon Ryan 104k

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Very cool, but I still got the same error.

ADD REPLY • link 10.0 years ago by xuzbnu • 0

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what's your command? Did you use the correct sra id?

ADD REPLY • link 10.0 years ago by Xingyu Yang ▴ 280

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According to this page: http://seqanswers.com/forums/showthread.php?t=13211, you need to update your sratools.

ADD REPLY • link updated 4.3 years ago by Ram 43k • written 10.0 years ago by Xingyu Yang ▴ 280