Downloading data from Short Read Archive

Dear all,

Does anyone know how I can download data from this page on Short Reach Archive?

https://www.ncbi.nlm.nih.gov/Traces/study/?acc=SRX1728385

Thanks.

sra short read archive

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updated 9.5 years ago by EagleEye

• written 9.5 years ago by biomagician

2 answers

Simply use SRA tools: https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3452286

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written 9.5 years ago by Michael Dondrup

Thanks it worked!

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written 9.5 years ago by biomagician

1) Download and install SRAtoolkit

2) Use fastq-dump to download SRA files as fastq files, (in your case SRR or run id is SRR3452286 )

fastq-dump --split-3 SRR3452286

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written 9.5 years ago by EagleEye

Thanks it worked! What's --split-3 for? I can't find it in the documentation. https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=toolkit_doc&f=fastq-dump The closest is --split-spot

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written 9.5 years ago by biomagician

Here is the answer in previously discussed post.

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written 9.5 years ago by EagleEye

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