*.sra files info

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5.5 years ago

tim.ivanov.92 ▴ 40

I've downloaded a lot of *sra archives, and I want to get information about the content of each of them. Can I do it without extracting every archive?

SRAToolkit next-gen • 946 views

ADD COMMENT • link updated 9 months ago by Ram 43k • written 5.5 years ago by tim.ivanov.92 ▴ 40

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What kind of information?

ADD REPLY • link 5.5 years ago by GenoMax 141k

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What is the content of the archive: is it unmapped reads (which i will need to align then) or is it already aligned *.sam file

ADD REPLY • link 5.5 years ago by tim.ivanov.92 ▴ 40

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You can pretty much assume that all SRA files contain unmapped reads. The ones that also contain mapped reads are pretty rare.

ADD REPLY • link 5.5 years ago by Devon Ryan 104k

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ok, thank you for the answer, then i'll just align them all

ADD REPLY • link 5.5 years ago by tim.ivanov.92 ▴ 40

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Take a look at sra-stat (and its options) from `sra-toolkit`` to see if that helps.

ADD REPLY • link 5.5 years ago by GenoMax 141k

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